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From: Justin E. <jus...@or...> - 2022-06-02 16:47:24
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
So, it definitely seems to be alphanumeric by the dataset_id. I
temporarily changed the Minghui63 id to 556 in both jbrowse.conf and
data/minghui63/tracks.conf and it is in the order I want. But, of
course, that breaks apollo.<br>
<br>
Because you asked though, here is the relevant bits of jbrowse.conf:<br>
<font face="monospace">[datasets.34]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.51]<br>
url = ?data=data/arc<br>
name = ARC<br>
[datasets.101]<br>
url = ?data=data/azucena<br>
name = Azucena<br>
[datasets.141]<br>
url = ?data=data/chaomeo<br>
name = Chao meo<br>
[datasets.225]<br>
url = ?data=data/gobolsailbalam<br>
name = Gobol Sail Balam<br>
[datasets.253]<br>
url = ?data=data/ir64<br>
name = IR64<br>
[datasets.276]<br>
url = ?data=data/ketan_nangka<br>
name = Ketan Nangka<br>
[datasets.304]<br>
url = ?data=data/khao_yai_guang<br>
name = Khao Yai Guang<br>
[datasets.332]<br>
url = ?data=data/larhamugad<br>
name = Larha Mugad<br>
[datasets.377]<br>
url = ?data=data/lima<br>
name = Lima<br>
[datasets.473]<br>
url = ?data=data/liuxu<br>
name = Liu Xu<br>
[datasets.1256]<br>
url = ?data=data/minghui63<br>
name = Minghui63<br>
[datasets.1051]<br>
url = ?data=data/nagina22<br>
name = Nagina 22<br>
[datasets.1159]<br>
url = ?data=data/natelboro<br>
name = Natel Boro<br>
[datasets.1181]<br>
url = ?data=data/pr106<br>
name = PR106<br>
[datasets.1224]<br>
url = ?data=data/zhenshan97<br>
name = Zhenshan97<br>
<br>
</font>And data/minghui63/tracks.conf:<br>
<font face="monospace">[general]<br>
dataset_id = 1256</font><br>
<font face="monospace"></font><br>
So, I guess the only way I can think of to change this is if it is
possible to change the apollo id from 1256 to something between 473
and 1051. But I'm guessing the reason that it jumps is that those
IDs are being used for something else internally.<br>
<br>
This is only a superficial issue, just something I was hoping to
clean up.<br>
<br>
I should also point out, Apollo has the dropdown selector in the top
left, and that matches the order they are in jbrowse, but on the
right side, they are purely in alphabetical order, so the order
doesn't match.<br>
<img src="cid:par...@or..." alt=""><br>
<br>
<img src="cid:par...@or..." alt=""><br>
<br>
Thanks,<br>
Justin<br>
<br>
<div class="moz-cite-prefix">On 6/1/22 3:52 PM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+...@ma...">
<p><span style="color:#D73F09;">[This email originated from
outside of OSU. Use caution with links and attachments.]</span></p>
<div>
<div dir="ltr">From my quick testing, I think the order in which
they are specified in the jbrowse.conf is the order in which
they will be listed in the Genome menu. I cannot guarantee
this would be the same situation for Apollo and am not aware
of any custom config to help this ordering in Apollo.
<div><br>
</div>
<div>If you have an example jbrowse.conf config where it
doesn't seem to be doing this in JBrowse though, feel free
to post</div>
<div><br>
</div>
<div><br>
</div>
<div>-Colin</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Jun 1, 2022 at 12:30
PM Justin Elser <<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>So, this is hopefully an easy question, and I may have
just missed it in the documentation, but is there a way to
change the order in which the datasets show up in the
genome selector?<br>
<br>
It looks like they get added in the order in which they
were added, or possibly alphanumeric by dataset_id?<br>
<br>
In the below screenshot, I'd like Minghui63 to be between
Liu Xu and Nagina 22, but since it is the last one I
added, it shows up last. I have it where I want it in the
jbrowse.conf file, but it still shows up last. I don't
totally want them in alphabetical order, as I would like
Nipponbare to be first.<br>
<img src="cid:par...@or..." alt="" class="" width="926" height="559"><br>
Is it possible to change this?<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/26/22 2:05 PM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This email
originated from outside of OSU. Use caution with
links and attachments.]</span></p>
<div>
<div dir="ltr">>Everything works as expected now! I
see both Nipponbare and ARC in the "Genome"
dropdown, and apollo is showing all data.<br>
<div><br>
</div>
<div>Excellent:)</div>
<div><br>
</div>
<div>>So, I guess apollo is only using the
numeric ID for the dataset instead of using what I
tried to set the dataset id? In other words, if I
had [datasets.nipponbare] in jbrowse.conf and
dataset_id=nipponbare in
data/nipponbare/tracks.conf, that is fine for
jbrowse, but apollo is only using it's internal ID
of 34?</div>
<div><br>
</div>
<div>You can inspect the database for the IDs, or
you can get the ID from inside the URL clicking
the link icon, see screenshot attachment here. I
don't think you can change the organism ID to
something else like a readable name unfortunately.</div>
<div><br>
</div>
<div>-Colin</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May 26,
2022 at 12:24 PM Justin Elser <<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Ok, I think I get it. At least, I think I can
get it working but I am a bit confused.<br>
<br>
So, I noticed in the apollo docker logs that I
see this:<br>
2022-05-26 18:10:34,589 [http-nio-8080-exec-4]
DEBUG apollo.PreferenceService - found organism
in session org.bbop.apollo.Organism : 34 so
returning<br>
2022-05-26 18:10:34,589 [http-nio-8080-exec-4]
DEBUG apollo.JbrowseController - got organism
org.bbop.apollo.Organism : 34 for client token
137967108160676781264638533<br>
2022-05-26 18:10:34,649 [http-nio-8080-exec-1]
DEBUG apollo.AnnotationEditorController -
handleOperation annotationEditor
get_sequence_alterations ->
getSequenceAlterations<br>
2022-05-26 18:10:34,650 [http-nio-8080-exec-1]
DEBUG apollo.PermissionService - dataObject
does not contain organism (may not be needed)<br>
2022-05-26 18:10:34,652 [http-nio-8080-exec-1]
DEBUG apollo.PreferenceService - found
in-memory preference:
{"id":96,"organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"currentOrganism":true,"nativeTrackList":true,"sequence":{"id":36,"name":"chr1","organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"length":43270923,"start":0,"end":43270923},"startbp":6587035,"endbp":7241056,"clientToken":"137967108160676781264638533","user":{"id":32,"username":<a href="mailto:ad...@lo..." target="_blank" moz-do-not-send="true">"ad...@lo..."</a>}}<br>
<br>
So, it looks like the apollo "id" is 34 for
Nipponbare, and similarly 51 for ARC.<br>
<br>
So, I changed the jbrowse.conf to have:<br>
[datasets.34]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.51]<br>
url = ?data=data/arc<br>
name = ARC<br>
and data/nipponbare/tracks.conf to have:<br>
[general]<br>
dataset_id = 34<br>
<br>
and similar change for data/arc/tracks.conf.<br>
<br>
Everything works as expected now! I see both
Nipponbare and ARC in the "Genome" dropdown, and
apollo is showing all data.<br>
<br>
So, I guess apollo is only using the numeric ID
for the dataset instead of using what I tried to
set the dataset id? In other words, if I had
[datasets.nipponbare] in jbrowse.conf and
dataset_id=nipponbare in
data/nipponbare/tracks.conf, that is fine for
jbrowse, but apollo is only using it's internal
ID of 34?<br>
<br>
I guess I just don't understand why apollo isn't
seeing the dataset_id I'm trying to set in
jbrowse instead of seeing it's own ID.<br>
<br>
How can I see what ID apollo is going to use
without just checking the logs and seeing what
it looks for? Or can I force it somehow to use
nipponbare instead of 34?<br>
<br>
Thanks for the info on JBrowse2/Apollo3, I'll
watch for updates.<br>
<br>
Justin<br>
<br>
<div>On 5/26/22 11:00 AM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from outside of OSU. Use
caution with links and attachments.]</span></p>
<div>
<div dir="ltr">
<div>The code that is crashing is probably
this, seeing renderDatasetSelector in
the stack trace</div>
<div><br>
</div>
<div><a href="https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216" originalsrc="https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216" shash="E4rBCDhvntfYmcPLoA4bTRk0ALPynaASLVv6ifsQS5i2x6Y8E7mmrc/N4PDm+R4+CwAUa2Or0bTagCEJzatbGOL0+mMDQhZSSMWieHxW6yoWVWM+H+nlNKo6Bq5yEdevnABEM6dVzFpOgxnoc7xUAiqaXEZWgcY+njYStd3UJsY=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216</a><br>
</div>
<div><br>
</div>
Since it is crashing there, I think maybe
your manually configured datasets are not
matching the Apollo configuration of the
datasets.
<div><br>
</div>
<div>If you make them match up, it might
fix it, and to do that, you may be able
to make the dataset ID be the organism
ID that Apollo gives. Would have to
update both the datasets and the
dataset_id</div>
<div><br>
</div>
<div>This is where Apollo sets the
dataset_id, uses organism ID <a href="https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440" originalsrc="https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440" shash="vKbL9PbscdUO7l35HXh/JqaQeIlLTE1h9+z4oHYYI47fZabwq7kuTX3Ig9niURlQxgmE6FKRRsXb8jNlcssa+gZ4yLmG4+iLG/9NCQwSCvHI4PtvdiyjMvaiO2IkxNLRfMz6i0zY2DFlBH7JOg386BPsMK/YPrWrYdXVPq6F80A=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440</a><br>
<div><br>
</div>
<div>To be clear, the dataset ID is what
is after the . in the conf format e.g.</div>
<div><br>
</div>
<div>[datasets.make_this_match_the_organismID]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Also, the current generation of
Apollo (Apollo 2) does not work with
JBrowse 2, but we are working on a new
Apollo version that will be integrated
with JBrowse 2. It's not ready for use
yet but you can keep an eye on <a href="https://github.com/GMOD/Apollo3" originalsrc="https://github.com/GMOD/Apollo3" shash="AgxOQvu5V1a6LPyQ2RkcjtIyow61Y/EnHlkyDlhQVvD1te6y8DflzHrrPXFUvEUQP2HWHcrAqIRcCKO3kr0auFit7rYkCZVFhplamnvwIPskskni+mZevmf/eNC2HYK94MvycXSTwLt827D3RuxmkJ4ypz3u7icElJCnEp7bvxY=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/Apollo3</a>
if interested</div>
<div><br>
</div>
<div>-Colin</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu,
May 26, 2022 at 9:56 AM Justin Elser
<<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>I'm attaching the output from the
chrome console. I don't think it's the
non-minified version of the JS though.
How would I get that with the docker
version of apollo?<br>
<br>
Also, I've been asked to ask if Apollo
works with JBrowse2? Would it be
better to use that instead of
JBrowse1?<br>
<br>
Thank you for taking the time to help
me.<br>
<br>
Justin<br>
<br>
<div>On 5/25/22 4:51 PM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from outside of
OSU. Use caution with links and
attachments.]</span></p>
<div>
<div dir="auto">The logs that are
probably most helpful are the
"JavaScript console" or
developer console from chrome or
firefox e.g.
<a href="https://balsamiq.com/support/faqs/browserconsole/" originalsrc="https://balsamiq.com/support/faqs/browserconsole/" shash="PI4oU9UZOXMgBHhYJ3y1MSpDM0qF8WdVy2MWaCXhWDXT9HuWUKo7fqTP8aQSBNEmnQY2j4PT0QXEVUMIc3D0PDmee6WLeaAHMF/V4+mHcSZux+u26h++/Vi5Zw4Vr74ff8zjOVvITe9qPRpK+1IHLkXHsqGhnxeRR6ls8Ny0vbY=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
https://balsamiq.com/support/faqs/browserconsole/</a></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May
25, 2022, 4:33 PM Justin Elser
<<a href="mailto:jus...@or..." rel="noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>We may just use Apollo to
serve both, but thought I
might give it a try to see
about JBrowse.<br>
<br>
I am attaching the output I
get when I run the docker
container with "-e
WEBAPOLLO_DEBUG=true".<br>
<br>
The blank lines are in
between it working and not
working. IE, lines 1-483 are
the initial startup and
navigating to the site with
Apollo working as expected.
Lines 487 on are after
changing
data/nipponbare/tracks.conf
to have:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
I do notice that after the
change it is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
(line 579) where it isn't
before. I don't understand
why it would be looking for
the sample data at all. I
never loaded it as a track
or anything.<br>
<br>
I also notice for the
initial load where it works
that it is complaining about
the mime_type for .bam
files. I did alter the
.htaccess for the jbrowse
but not apollo, so I think
those are fixable and
unrelated. Weirdly enough,
the bam track does load fine
in Apollo where it didn't in
JBrowse until I made the
change to .htaccess.<br>
<br>
If you meant some other
logs, please let me know how
to get those and I will send
them to you.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22 2:18 PM,
Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from
outside of OSU. Use
caution with links and
attachments.]</span></p>
<div>
<div dir="ltr">One
option is to use
Apollo to serve your
jbrowse instances,
Apollo can serve
public jbrowse
instances so you may
not need to configure
jbrowse separately
<div><br>
</div>
<div><br>
<div>If you do want
it separate, then
we would probably
need to debug that
error. If you have
the stack trace
from the developer
console, it might
narrow down
exactly where the
error comes from.
If the stack trace
is minified and
hard to read, can
possibly use a
"dev" version of
jbrowse if it is
too unreadable
since it does not
minify the builds!
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On
Wed, May 25, 2022 at
1:03 PM Justin Elser
<<a href="mailto:jus...@or..." rel="noreferrer
noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex">
<div>Yeah, so I
guess the problem
is that if I don't
add the
"dataset_id" to
each
data/(species)/tracks.conf
file, apollo works
fine, but then I
can't get the
dataset selector
in jbrowse. As I
have it right now,
Apollo is fine,
but I have no way
to switch to a
different dataset
in JBrowse.<br>
<img alt="" moz-do-not-send="true" width="1073" height="648"><br>
<br>
I was messing
around with
jbrowse.conf,
data/tracks.conf,
and
data/(species)/tracks.conf,
and was able to
get a list of the
species under the
"Genome" tab. But
if I don't have
anything in
data/(species)/tracks.conf,
I don't. However,
if I do add it
like in the
documentation, the
species are listed
under there:<br>
<img alt="" moz-do-not-send="true" width="1021" height="616"><br>
But then, apollo
breaks:<br>
<img alt="" moz-do-not-send="true" width="972" height="587"><br>
<br>
So, I guess I need
to get the
dataset_selector
working in
JBrowse, while not
breaking Apollo.<br>
<br>
I hope that clears
it up more.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22
11:50 AM, Colin
wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email
originated
from outside
of OSU. Use
caution with
links and
attachments.]</span></p>
<div>
<div dir="ltr">
<div>I haven't
evaluated the
whole post
here, but note
that Apollo
automatically
creates a
dataset
selector from
assemblies
that you
configure
through that
Apollo
interface</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 25, 2022 at 12:21 PM Justin Elser <<a href="mailto:jus...@or..." rel="noreferrer noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Hi all,<br>
<br>
I have set up
a jbrowse
1.16.11
instance
(sorry, not
publicly
available) <br>
and added 2
species (well,
different
cultivars) by
doing the
following:<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="eKfzIvGOov0xH/TztMmSjKrQpagJMfaZpnyIcUjkh7a17jXlYKzcYJTAT5Bxhhvmd21OXPZZIeY9zOHBE8u91QxK8XoDYGaFnq+6BWC2gcMlbwzjhrZuyu75OcNUEKGnbRM/pYlAE925HG11dxTWRftQnYorTx1aNnEEuCISFhs=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a> --out data/nipponbare
--fasta <br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="tcXk3DVnk7wf4j/Trwbns8JwOHzHdX/2h2rm4acpYihs6opONa0mjFAN2qVtm8a+4+6HQPrbdmrmglDHIHz+fgeoER1cX6/vGpRewQrgKUIP6F1SzLE3QzXPqGImqL66ePPerqZ2QiER/UB4c+Wh1gyWyNCvv2g2Wd0VSHCPGQQ=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a> --out data/nipponbare
--trackType
CanvasFeatures
<br>
--trackLabel
MSU7.0 -gff
source_files/MSU7.0.gff3<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="k1460HP/ir4tRnQRm8QXtl7L1nL/FH1vQSyA2G8a5uvGjGkNvSgC9E+rPqK4EaY0i0J/ak2LsP9wSJtl9pfqBNBVvdds1ds1eDMvhLvir5ENmawbzw1yv/wfAfpJNWam7oplw8O6zMmTLHqKNEmZNhKaBRSWJckUWvtMxkAS5dY=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a> --out data/nipponbare<br>
<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="eKfzIvGOov0xH/TztMmSjKrQpagJMfaZpnyIcUjkh7a17jXlYKzcYJTAT5Bxhhvmd21OXPZZIeY9zOHBE8u91QxK8XoDYGaFnq+6BWC2gcMlbwzjhrZuyu75OcNUEKGnbRM/pYlAE925HG11dxTWRftQnYorTx1aNnEEuCISFhs=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a> --out data/arc --fasta <br>
source_files/magic_16/oryza_sativa_arc.fa<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="tcXk3DVnk7wf4j/Trwbns8JwOHzHdX/2h2rm4acpYihs6opONa0mjFAN2qVtm8a+4+6HQPrbdmrmglDHIHz+fgeoER1cX6/vGpRewQrgKUIP6F1SzLE3QzXPqGImqL66ePPerqZ2QiER/UB4c+Wh1gyWyNCvv2g2Wd0VSHCPGQQ=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a> --out data/arc
--trackType
CanvasFeatures
<br>
--trackLabel
Genes -gff
source_files/magic_16/oryza_sativa_arc.gff<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="k1460HP/ir4tRnQRm8QXtl7L1nL/FH1vQSyA2G8a5uvGjGkNvSgC9E+rPqK4EaY0i0J/ak2LsP9wSJtl9pfqBNBVvdds1ds1eDMvhLvir5ENmawbzw1yv/wfAfpJNWam7oplw8O6zMmTLHqKNEmZNhKaBRSWJckUWvtMxkAS5dY=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a> --out data/arc<br>
<br>
Then I edited
the
jbrowse.conf
file as
explained in <br>
<a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="qRZdKZN2NokNLP4IemLR4xIRv9iMhhlJEGU6IbWXJEbIMuT1T8PeH5+UOJWe7xDb/YXoJjYVvSXNVdE9W4zUsRtITCClHFNZP9KvdJ1TGyg1XdI9uMxQiGTdDvoaFK2/nziq2wk2ChDnRFtir9T4/FNC+bSl49NTVjaQ3s4m/pk=" rel="noreferrer noreferrer noreferrer noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
to have:<br>
dataRoot =
data/nipponbare<br>
[datasets.nipponbare]<br>
url =
?data=data/nipponbare<br>
name =
Nipponbare<br>
[datasets.arc]<br>
url =
?data=data/arc<br>
name = ARC<br>
<br>
And all seems
to work fine,
except that I
don't see the
dropdown to <br>
switch
datasets, so I
can't actually
see the ARC
dataset.
Although I <br>
have by
messing around
with
jbrowse.conf
and
tracks.conf
gotten it to <br>
work, but at
this point
I've left it
out.<br>
<br>
However, the
issue I'm
having is
actually with
Apollo. I have
the docker <br>
instance of
apollo running
and it seems
to be fine as
configured in
a <br>
systemd unit
file:<br>
ExecStart=/usr/bin/docker run --rm --name %n \<br>
-e
APOLLO_PATH=apollo
\<br>
-v
/data/www/panoryza/jbrowse/<a rel="noreferrer noreferrer noreferrer" moz-do-not-send="true">data:/data</a>
\<br>
-v
/data/www/panoryza/apollo/postgres:/var/lib/postgresql
\<br>
-v <br>
/data/www/panoryza/apollo/apollo_<a rel="noreferrer noreferrer
noreferrer" moz-do-not-send="true">data:/data/temporary/apollo_data</a>
\<br>
-p
8887:8080 \<br>
gmod/apollo:latest<br>
<br>
Adding
Nipponbare as
an organism
with
"Directory"
/data/nipponbare
works <br>
fine and I can
see the tracks
I've added.<br>
<br>
Now, here is
where the
issue I have
starts. If I
edit the <br>
data/nipponbare/tracks.conf file as shown in the dataset selector <br>
documentation
above:<br>
[general]<br>
dataset_id =
nipponbare<br>
<br>
Apollo then
shows the
following
error:<br>
Error
message(s):<br>
TypeError:
Cannot read
properties of
undefined
(reading
'name').<br>
<br>
Clearing out
the
data/nipponbare/tracks.conf
file allows
apollo to
work.<br>
Now, the error
only appears
in apollo,
jbrowse works
fine with the
edits.<br>
<br>
I'm a bit
confused about
how this
should be
configured to
work. I <br>
actually have
14 more
"species" to
add, but
waiting till I
at least get <br>
it working
with one. The
documentation
isn't clear to
me on the <br>
difference
between adding
the datasets
to
jbrowse.conf
vs <br>
data/tracks.conf vs data/(species)/tracks.conf.<br>
<br>
Please let me
know if you
need any more
information.<br>
<br>
Thanks,<br>
Justin<br>
<br>
-- <br>
**********************************************************<br>
*
*<br>
* Justin
Elser
*<br>
*
Computational
Biology
Research
Associate
*<br>
* Dept. of
Botany and
Plant
Pathology
*<br>
* Jaiswal
Lab
*<br>
* Oregon
State
University
*<br>
*
*<br>
* email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
jus...@or...</a> *<br>
*
*<br>
**********************************************************<br>
<br>
<br>
<br>
_______________________________________________<br>
Gmod-ajax
mailing list<br>
<a href="mailto:Gmo...@li..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
<a href="https://lists...
[truncated message content] |
|
From: Nathan D. <nd...@gm...> - 2022-06-02 15:36:26
|
I would download and install JBrowse 1 and generate the names with that perl script and then point your Apollo organism directory there. That’s been more reliable for me in general. Nathan > On Jun 1, 2022, at 9:20 PM, Johannes Debler <joh...@gm...> wrote: > > Thanks Nathan, > > I can't really figure out how to run it, or what the input is meant to be. > I have a file called 'trackList.json' which contains all the tracks. > > But when I run this command: > generate-names.pl <http://generate-names.pl/> --tracks trackList.json > > I get a bunch of errors: > syntax error in /home/data/apollo_data/36-AlKewell/data/trackList.json: malformed JSON string, neither tag, array, object, number, string or atom, at character offset 0 (before "(end of string)") at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32. > at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7. > Bio::JBrowse::ConfigurationManager::__ANON__("malformed JSON string, neither tag, array, object, number, st"...) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32 > eval {...} called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32 > Bio::JBrowse::ConfigurationManager::slurpJSON("/home/data/apollo_data/36-AlKewell/data/trackList.json") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 145 > Bio::JBrowse::ConfigurationManager::_load_include(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x55984670af60), "data") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 71 > Bio::JBrowse::ConfigurationManager::_load_includes(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x559845add2c8)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 41 > Bio::JBrowse::ConfigurationManager::get_final_config(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/GenomeDB.pm line 261 > GenomeDB::refSeqs(GenomeDB=HASH(0x55984670b518)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/IndexNames.pm line 77 > Bio::JBrowse::Cmd::IndexNames::run(Bio::JBrowse::Cmd::IndexNames=HASH(0x559845b08060)) called at /opt/Apollo-2.6.5/jbrowse/bin/generate-names.pl <http://generate-names.pl/> line 8 > at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7. > Bio::JBrowse::ConfigurationManager::__ANON__("syntax error in /home/data/apollo_data/36-AlKewell/data/track"...) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 33 > Bio::JBrowse::ConfigurationManager::slurpJSON("/home/data/apollo_data/36-AlKewell/data/trackList.json") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 145 > Bio::JBrowse::ConfigurationManager::_load_include(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x55984670af60), "data") called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 71 > Bio::JBrowse::ConfigurationManager::_load_includes(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900), HASH(0x559845add2c8)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 41 > Bio::JBrowse::ConfigurationManager::get_final_config(Bio::JBrowse::ConfigurationManager=HASH(0x55984670a900)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/GenomeDB.pm line 261 > GenomeDB::refSeqs(GenomeDB=HASH(0x55984670b518)) called at /opt/Apollo-2.6.5/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/IndexNames.pm line 77 > Bio::JBrowse::Cmd::IndexNames::run(Bio::JBrowse::Cmd::IndexNames=HASH(0x559845b08060)) called at /opt/Apollo-2.6.5/jbrowse/bin/generate-names.pl <http://generate-names.pl/> line 8 > > Not sure if this is the correct way to run the script in the first place, but the help doesn't go into much detail unfortunately. > > Cheers, > Johannes > > On Thu, 2 Jun 2022 at 11:37, Nathan Dunn <nd...@gm... <mailto:nd...@gm...>> wrote: > > If you use generate-names: https://jbrowse.org/docs/generate-names.pl.html <https://jbrowse.org/docs/generate-names.pl.html> > > You should be able to search for genes, etc. in the location box. > > e.g., https://jbrowse.org/jbrowse1.html <https://jbrowse.org/jbrowse1.html> use the search box to look for Apple3. > > Nathan > >> On Jun 1, 2022, at 8:28 PM, Johannes Debler <joh...@gm... <mailto:joh...@gm...>> wrote: >> >> Hi, >> I was wondering if it is possible to search annotations in tracks other than 'User-created Annotations'. >> I have finished annotating my genome and would now like to get rid of all the models in the 'User-created Annotations' track and only display my final annotations track. >> >> Currently if I try to search for a gene name in the 'Annotations' tab, it only finds things in the 'User-created Annotations' track. Is there a way to make the other tracks searchable, or alternatively, remove all annotations from the 'User....' track and upload my final annotations to that track. >> >> Cheers, >> Johannes >> >> -- >> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>. > |
|
From: Vaneet L. <van...@uc...> - 2022-06-02 15:04:47
|
Thanks Colin, that's good to know. Vaneet ________________________________ From: Colin <col...@gm...> Sent: June 1, 2022 4:43 PM To: Vaneet Lotay <van...@uc...> Cc: gmo...@li... <gmo...@li...> Subject: Re: [Gmod-ajax] JBrowse XML parsing errors [△EXTERNAL] Hi Vaneet, This console log message is just a browser specific thing with Firefox, but as far as I know does not indicate anything is wrong. It is just something Firefox says when a .conf file is downloaded, but the .conf file is otherwise interpreted fine by the JBrowse code itself. I think you can ignore the message -Colin On Wed, Jun 1, 2022 at 11:59 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hi, I attached a screenshot of the XML parsing errors from the console of my Firefox browser, which I'm a little confused about. I checked the actual configuration files that these errors denote, and I don't see anything wrong or any hidden characters that are there on the first line. I don't think these are file specific though as no matter what genome I switch to in JBrowse I see the same errors, that is those genomes for which I have an extra configuration file for functions that's named 'functions.conf'. The jbrowse.conf error always appears. I don't see any visible problem on the browser tracks that results from these errors but I just want to eliminate them to make sure. After looking at the JBrowse 1 troubleshooting page, I took the suggestion to install the libexpat1-dev package and then rerun the setup.sh script, but errors are still there on Firefox. If I load the page in Microsoft Edge browser, I don't see the errors there, so I'm wondering if it's browser specific? Is anyone aware of any fixes for this specific issue? Thanks, Vaneet _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
|
From: Colin <col...@gm...> - 2022-06-01 22:52:41
|
>From my quick testing, I think the order in which they are specified in the
jbrowse.conf is the order in which they will be listed in the Genome menu.
I cannot guarantee this would be the same situation for Apollo and am not
aware of any custom config to help this ordering in Apollo.
If you have an example jbrowse.conf config where it doesn't seem to be
doing this in JBrowse though, feel free to post
-Colin
On Wed, Jun 1, 2022 at 12:30 PM Justin Elser <jus...@or...>
wrote:
> So, this is hopefully an easy question, and I may have just missed it in
> the documentation, but is there a way to change the order in which the
> datasets show up in the genome selector?
>
> It looks like they get added in the order in which they were added, or
> possibly alphanumeric by dataset_id?
>
> In the below screenshot, I'd like Minghui63 to be between Liu Xu and
> Nagina 22, but since it is the last one I added, it shows up last. I have
> it where I want it in the jbrowse.conf file, but it still shows up last. I
> don't totally want them in alphabetical order, as I would like Nipponbare
> to be first.
>
> Is it possible to change this?
>
> Thanks,
> Justin
>
> On 5/26/22 2:05 PM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> >Everything works as expected now! I see both Nipponbare and ARC in the
> "Genome" dropdown, and apollo is showing all data.
>
> Excellent:)
>
> >So, I guess apollo is only using the numeric ID for the dataset instead
> of using what I tried to set the dataset id? In other words, if I had
> [datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
> data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
> using it's internal ID of 34?
>
> You can inspect the database for the IDs, or you can get the ID from
> inside the URL clicking the link icon, see screenshot attachment here. I
> don't think you can change the organism ID to something else like a
> readable name unfortunately.
>
> -Colin
>
> On Thu, May 26, 2022 at 12:24 PM Justin Elser <
> jus...@or...> wrote:
>
>> Ok, I think I get it. At least, I think I can get it working but I am a
>> bit confused.
>>
>> So, I noticed in the apollo docker logs that I see this:
>> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
>> apollo.PreferenceService - found organism in session
>> org.bbop.apollo.Organism : 34 so returning
>> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
>> apollo.JbrowseController - got organism org.bbop.apollo.Organism : 34 for
>> client token 137967108160676781264638533
>> 2022-05-26 18:10:34,649 [http-nio-8080-exec-1] DEBUG
>> apollo.AnnotationEditorController - handleOperation annotationEditor
>> get_sequence_alterations -> getSequenceAlterations
>> 2022-05-26 18:10:34,650 [http-nio-8080-exec-1] DEBUG
>> apollo.PermissionService - dataObject does not contain organism (may not
>> be needed)
>> 2022-05-26 18:10:34,652 [http-nio-8080-exec-1] DEBUG
>> apollo.PreferenceService - found in-memory preference:
>> {"id":96,"organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"currentOrganism":true,"nativeTrackList":true,"sequence":{"id":36,"name":"chr1","organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"length":43270923,"start":0,"end":43270923},"startbp":6587035,"endbp":7241056,"clientToken":"137967108160676781264638533","user":{"id":32,"username":
>> "ad...@lo..." <ad...@lo...>}}
>>
>> So, it looks like the apollo "id" is 34 for Nipponbare, and similarly 51
>> for ARC.
>>
>> So, I changed the jbrowse.conf to have:
>> [datasets.34]
>> url = ?data=data/nipponbare
>> name = Nipponbare
>> [datasets.51]
>> url = ?data=data/arc
>> name = ARC
>> and data/nipponbare/tracks.conf to have:
>> [general]
>> dataset_id = 34
>>
>> and similar change for data/arc/tracks.conf.
>>
>> Everything works as expected now! I see both Nipponbare and ARC in the
>> "Genome" dropdown, and apollo is showing all data.
>>
>> So, I guess apollo is only using the numeric ID for the dataset instead
>> of using what I tried to set the dataset id? In other words, if I had
>> [datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
>> data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
>> using it's internal ID of 34?
>>
>> I guess I just don't understand why apollo isn't seeing the dataset_id
>> I'm trying to set in jbrowse instead of seeing it's own ID.
>>
>> How can I see what ID apollo is going to use without just checking the
>> logs and seeing what it looks for? Or can I force it somehow to use
>> nipponbare instead of 34?
>>
>> Thanks for the info on JBrowse2/Apollo3, I'll watch for updates.
>>
>> Justin
>>
>> On 5/26/22 11:00 AM, Colin wrote:
>>
>> [This email originated from outside of OSU. Use caution with links and
>> attachments.]
>> The code that is crashing is probably this, seeing renderDatasetSelector
>> in the stack trace
>>
>>
>> https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216
>>
>> Since it is crashing there, I think maybe your manually configured
>> datasets are not matching the Apollo configuration of the datasets.
>>
>> If you make them match up, it might fix it, and to do that, you may be
>> able to make the dataset ID be the organism ID that Apollo gives. Would
>> have to update both the datasets and the dataset_id
>>
>> This is where Apollo sets the dataset_id, uses organism ID
>> https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440
>>
>> To be clear, the dataset ID is what is after the . in the conf format e.g.
>>
>> [datasets.make_this_match_the_organismID]
>> url = ?data=data/nipponbare
>> name = Nipponbare
>>
>>
>> Also, the current generation of Apollo (Apollo 2) does not work with
>> JBrowse 2, but we are working on a new Apollo version that will be
>> integrated with JBrowse 2. It's not ready for use yet but you can keep an
>> eye on https://github.com/GMOD/Apollo3 if interested
>>
>> -Colin
>>
>>
>>
>> On Thu, May 26, 2022 at 9:56 AM Justin Elser <
>> jus...@or...> wrote:
>>
>>> I'm attaching the output from the chrome console. I don't think it's the
>>> non-minified version of the JS though. How would I get that with the docker
>>> version of apollo?
>>>
>>> Also, I've been asked to ask if Apollo works with JBrowse2? Would it be
>>> better to use that instead of JBrowse1?
>>>
>>> Thank you for taking the time to help me.
>>>
>>> Justin
>>>
>>> On 5/25/22 4:51 PM, Colin wrote:
>>>
>>> [This email originated from outside of OSU. Use caution with links and
>>> attachments.]
>>> The logs that are probably most helpful are the "JavaScript console" or
>>> developer console from chrome or firefox e.g.
>>> https://balsamiq.com/support/faqs/browserconsole/
>>>
>>> On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...>
>>> wrote:
>>>
>>>> We may just use Apollo to serve both, but thought I might give it a try
>>>> to see about JBrowse.
>>>>
>>>> I am attaching the output I get when I run the docker container with
>>>> "-e WEBAPOLLO_DEBUG=true".
>>>>
>>>> The blank lines are in between it working and not working. IE, lines
>>>> 1-483 are the initial startup and navigating to the site with Apollo
>>>> working as expected. Lines 487 on are after changing
>>>> data/nipponbare/tracks.conf to have:
>>>> [general]
>>>> dataset_id = nipponbare
>>>>
>>>> I do notice that after the change it is trying to open
>>>> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
>>>> (line 579) where it isn't before. I don't understand why it would be
>>>> looking for the sample data at all. I never loaded it as a track or
>>>> anything.
>>>>
>>>> I also notice for the initial load where it works that it is
>>>> complaining about the mime_type for .bam files. I did alter the .htaccess
>>>> for the jbrowse but not apollo, so I think those are fixable and unrelated.
>>>> Weirdly enough, the bam track does load fine in Apollo where it didn't in
>>>> JBrowse until I made the change to .htaccess.
>>>>
>>>> If you meant some other logs, please let me know how to get those and I
>>>> will send them to you.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On 5/25/22 2:18 PM, Colin wrote:
>>>>
>>>> [This email originated from outside of OSU. Use caution with links and
>>>> attachments.]
>>>> One option is to use Apollo to serve your jbrowse instances, Apollo can
>>>> serve public jbrowse instances so you may not need to configure jbrowse
>>>> separately
>>>>
>>>>
>>>> If you do want it separate, then we would probably need to debug that
>>>> error. If you have the stack trace from the developer console, it might
>>>> narrow down exactly where the error comes from. If the stack trace is
>>>> minified and hard to read, can possibly use a "dev" version of jbrowse if
>>>> it is too unreadable since it does not minify the builds!
>>>>
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Wed, May 25, 2022 at 1:03 PM Justin Elser <
>>>> jus...@or...> wrote:
>>>>
>>>>> Yeah, so I guess the problem is that if I don't add the "dataset_id"
>>>>> to each data/(species)/tracks.conf file, apollo works fine, but then I
>>>>> can't get the dataset selector in jbrowse. As I have it right now, Apollo
>>>>> is fine, but I have no way to switch to a different dataset in JBrowse.
>>>>>
>>>>>
>>>>> I was messing around with jbrowse.conf, data/tracks.conf, and
>>>>> data/(species)/tracks.conf, and was able to get a list of the species under
>>>>> the "Genome" tab. But if I don't have anything in
>>>>> data/(species)/tracks.conf, I don't. However, if I do add it like in the
>>>>> documentation, the species are listed under there:
>>>>>
>>>>> But then, apollo breaks:
>>>>>
>>>>>
>>>>> So, I guess I need to get the dataset_selector working in JBrowse,
>>>>> while not breaking Apollo.
>>>>>
>>>>> I hope that clears it up more.
>>>>>
>>>>> Thanks,
>>>>> Justin
>>>>>
>>>>> On 5/25/22 11:50 AM, Colin wrote:
>>>>>
>>>>> [This email originated from outside of OSU. Use caution with links and
>>>>> attachments.]
>>>>> I haven't evaluated the whole post here, but note that Apollo
>>>>> automatically creates a dataset selector from assemblies that you configure
>>>>> through that Apollo interface
>>>>>
>>>>>
>>>>> -Colin
>>>>>
>>>>> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
>>>>> jus...@or...> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly
>>>>>> available)
>>>>>> and added 2 species (well, different cultivars) by doing the
>>>>>> following:
>>>>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>>>>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>>>>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType
>>>>>> CanvasFeatures
>>>>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>>>>>> bin/generate-names.pl --out data/nipponbare
>>>>>>
>>>>>> bin/prepare-refseqs.pl --out data/arc --fasta
>>>>>> source_files/magic_16/oryza_sativa_arc.fa
>>>>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>>>>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>>>>>> bin/generate-names.pl --out data/arc
>>>>>>
>>>>>> Then I edited the jbrowse.conf file as explained in
>>>>>> https://jbrowse.org/docs/dataset_selector.html to have:
>>>>>> dataRoot = data/nipponbare
>>>>>> [datasets.nipponbare]
>>>>>> url = ?data=data/nipponbare
>>>>>> name = Nipponbare
>>>>>> [datasets.arc]
>>>>>> url = ?data=data/arc
>>>>>> name = ARC
>>>>>>
>>>>>> And all seems to work fine, except that I don't see the dropdown to
>>>>>> switch datasets, so I can't actually see the ARC dataset. Although I
>>>>>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>>>>>> work, but at this point I've left it out.
>>>>>>
>>>>>> However, the issue I'm having is actually with Apollo. I have the
>>>>>> docker
>>>>>> instance of apollo running and it seems to be fine as configured in a
>>>>>> systemd unit file:
>>>>>> ExecStart=/usr/bin/docker run --rm --name %n \
>>>>>> -e APOLLO_PATH=apollo \
>>>>>> -v /data/www/panoryza/jbrowse/data:/data \
>>>>>> -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>>>>> -v
>>>>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>>>>> -p 8887:8080 \
>>>>>> gmod/apollo:latest
>>>>>>
>>>>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare
>>>>>> works
>>>>>> fine and I can see the tracks I've added.
>>>>>>
>>>>>> Now, here is where the issue I have starts. If I edit the
>>>>>> data/nipponbare/tracks.conf file as shown in the dataset selector
>>>>>> documentation above:
>>>>>> [general]
>>>>>> dataset_id = nipponbare
>>>>>>
>>>>>> Apollo then shows the following error:
>>>>>> Error message(s):
>>>>>> TypeError: Cannot read properties of undefined (reading 'name').
>>>>>>
>>>>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to
>>>>>> work.
>>>>>> Now, the error only appears in apollo, jbrowse works fine with the
>>>>>> edits.
>>>>>>
>>>>>> I'm a bit confused about how this should be configured to work. I
>>>>>> actually have 14 more "species" to add, but waiting till I at least
>>>>>> get
>>>>>> it working with one. The documentation isn't clear to me on the
>>>>>> difference between adding the datasets to jbrowse.conf vs
>>>>>> data/tracks.conf vs data/(species)/tracks.conf.
>>>>>>
>>>>>> Please let me know if you need any more information.
>>>>>>
>>>>>> Thanks,
>>>>>> Justin
>>>>>>
>>>>>> --
>>>>>> **********************************************************
>>>>>> * *
>>>>>> * Justin Elser *
>>>>>> * Computational Biology Research Associate *
>>>>>> * Dept. of Botany and Plant Pathology *
>>>>>> * Jaiswal Lab *
>>>>>> * Oregon State University *
>>>>>> * *
>>>>>> * email: jus...@or... *
>>>>>> * *
>>>>>> **********************************************************
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>
>>>>> --
>>>>> **********************************************************
>>>>> * *
>>>>> * Justin Elser *
>>>>> * Computational Biology Research Associate *
>>>>> * Dept. of Botany and Plant Pathology *
>>>>> * Jaiswal Lab *
>>>>> * Oregon State University *
>>>>> * *
>>>>> * email: jus...@or... *
>>>>> * *
>>>>> **********************************************************
>>>>>
>>>>>
>>>> --
>>>> **********************************************************
>>>> * *
>>>> * Justin Elser *
>>>> * Computational Biology Research Associate *
>>>> * Dept. of Botany and Plant Pathology *
>>>> * Jaiswal Lab *
>>>> * Oregon State University *
>>>> * *
>>>> * email: jus...@or... *
>>>> * *
>>>> **********************************************************
>>>>
>>>>
>>> --
>>> **********************************************************
>>> * *
>>> * Justin Elser *
>>> * Computational Biology Research Associate *
>>> * Dept. of Botany and Plant Pathology *
>>> * Jaiswal Lab *
>>> * Oregon State University *
>>> * *
>>> * email: jus...@or... *
>>> * *
>>> **********************************************************
>>>
>>>
>> --
>> **********************************************************
>> * *
>> * Justin Elser *
>> * Computational Biology Research Associate *
>> * Dept. of Botany and Plant Pathology *
>> * Jaiswal Lab *
>> * Oregon State University *
>> * *
>> * email: jus...@or... *
>> * *
>> **********************************************************
>>
>>
> --
> **********************************************************
> * *
> * Justin Elser *
> * Computational Biology Research Associate *
> * Dept. of Botany and Plant Pathology *
> * Jaiswal Lab *
> * Oregon State University *
> * *
> * email: jus...@or... *
> * *
> **********************************************************
>
>
|
|
From: Colin <col...@gm...> - 2022-06-01 22:44:01
|
Hi Vaneet, This console log message is just a browser specific thing with Firefox, but as far as I know does not indicate anything is wrong. It is just something Firefox says when a .conf file is downloaded, but the .conf file is otherwise interpreted fine by the JBrowse code itself. I think you can ignore the message -Colin On Wed, Jun 1, 2022 at 11:59 AM Vaneet Lotay <van...@uc...> wrote: > Hi, > > I attached a screenshot of the XML parsing errors from the console of my > Firefox browser, which I'm a little confused about. I checked the actual > configuration files that these errors denote, and I don't see anything > wrong or any hidden characters that are there on the first line. I don't > think these are file specific though as no matter what genome I switch to > in JBrowse I see the same errors, that is those genomes for which I have an > extra configuration file for functions that's named 'functions.conf'. The > jbrowse.conf error always appears. I don't see any visible problem on the > browser tracks that results from these errors but I just want to eliminate > them to make sure. > > After looking at the JBrowse 1 troubleshooting page, I took the suggestion > to install the libexpat1-dev package and then rerun the setup.sh script, > but errors are still there on Firefox. If I load the page in Microsoft > Edge browser, I don't see the errors there, so I'm wondering if it's > browser specific? Is anyone aware of any fixes for this specific issue? > > Thanks, > > Vaneet > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Justin E. <jus...@or...> - 2022-06-01 21:04:55
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
So, this is hopefully an easy question, and I may have just missed
it in the documentation, but is there a way to change the order in
which the datasets show up in the genome selector?<br>
<br>
It looks like they get added in the order in which they were added,
or possibly alphanumeric by dataset_id?<br>
<br>
In the below screenshot, I'd like Minghui63 to be between Liu Xu and
Nagina 22, but since it is the last one I added, it shows up last. I
have it where I want it in the jbrowse.conf file, but it still shows
up last. I don't totally want them in alphabetical order, as I would
like Nipponbare to be first.<br>
<img src="cid:par...@or..." alt="" width="926" height="559"><br>
Is it possible to change this?<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div class="moz-cite-prefix">On 5/26/22 2:05 PM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+...@ma...">
<p><span style="color:#D73F09;">[This email originated from
outside of OSU. Use caution with links and attachments.]</span></p>
<div>
<div dir="ltr">>Everything works as expected now! I see both
Nipponbare and ARC in the "Genome" dropdown, and apollo is
showing all data.<br>
<div><br>
</div>
<div>Excellent:)</div>
<div><br>
</div>
<div>>So, I guess apollo is only using the numeric ID for
the dataset instead of using what I tried to set the dataset
id? In other words, if I had [datasets.nipponbare] in
jbrowse.conf and dataset_id=nipponbare in
data/nipponbare/tracks.conf, that is fine for jbrowse, but
apollo is only using it's internal ID of 34?</div>
<div><br>
</div>
<div>You can inspect the database for the IDs, or you can get
the ID from inside the URL clicking the link icon, see
screenshot attachment here. I don't think you can change the
organism ID to something else like a readable name
unfortunately.</div>
<div><br>
</div>
<div>-Colin</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May 26, 2022 at
12:24 PM Justin Elser <<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Ok, I think I get it. At least, I think I can get it
working but I am a bit confused.<br>
<br>
So, I noticed in the apollo docker logs that I see this:<br>
2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
apollo.PreferenceService - found organism in session
org.bbop.apollo.Organism : 34 so returning<br>
2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
apollo.JbrowseController - got organism
org.bbop.apollo.Organism : 34 for client token
137967108160676781264638533<br>
2022-05-26 18:10:34,649 [http-nio-8080-exec-1] DEBUG
apollo.AnnotationEditorController - handleOperation
annotationEditor get_sequence_alterations ->
getSequenceAlterations<br>
2022-05-26 18:10:34,650 [http-nio-8080-exec-1] DEBUG
apollo.PermissionService - dataObject does not contain
organism (may not be needed)<br>
2022-05-26 18:10:34,652 [http-nio-8080-exec-1] DEBUG
apollo.PreferenceService - found in-memory preference:
{"id":96,"organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"currentOrganism":true,"nativeTrackList":true,"sequence":{"id":36,"name":"chr1","organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"length":43270923,"start":0,"end":43270923},"startbp":6587035,"endbp":7241056,"clientToken":"137967108160676781264638533","user":{"id":32,"username":<a href="mailto:ad...@lo..." target="_blank" moz-do-not-send="true">"ad...@lo..."</a>}}<br>
<br>
So, it looks like the apollo "id" is 34 for Nipponbare,
and similarly 51 for ARC.<br>
<br>
So, I changed the jbrowse.conf to have:<br>
[datasets.34]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.51]<br>
url = ?data=data/arc<br>
name = ARC<br>
and data/nipponbare/tracks.conf to have:<br>
[general]<br>
dataset_id = 34<br>
<br>
and similar change for data/arc/tracks.conf.<br>
<br>
Everything works as expected now! I see both Nipponbare
and ARC in the "Genome" dropdown, and apollo is showing
all data.<br>
<br>
So, I guess apollo is only using the numeric ID for the
dataset instead of using what I tried to set the dataset
id? In other words, if I had [datasets.nipponbare] in
jbrowse.conf and dataset_id=nipponbare in
data/nipponbare/tracks.conf, that is fine for jbrowse, but
apollo is only using it's internal ID of 34?<br>
<br>
I guess I just don't understand why apollo isn't seeing
the dataset_id I'm trying to set in jbrowse instead of
seeing it's own ID.<br>
<br>
How can I see what ID apollo is going to use without just
checking the logs and seeing what it looks for? Or can I
force it somehow to use nipponbare instead of 34?<br>
<br>
Thanks for the info on JBrowse2/Apollo3, I'll watch for
updates.<br>
<br>
Justin<br>
<br>
<div>On 5/26/22 11:00 AM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This email
originated from outside of OSU. Use caution with
links and attachments.]</span></p>
<div>
<div dir="ltr">
<div>The code that is crashing is probably this,
seeing renderDatasetSelector in the stack trace</div>
<div><br>
</div>
<div><a href="https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216" originalsrc="https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216" shash="uhjL/hW/sjvOdWW3sAmi7MXxNww/o/kUrVgnDjMwc8zMNV4To9B20gCN/oqOaByxVsHC7IkHHs85yF8qz4KWCNInA+Rxto66yUepLZLhE8P0JFq7MctzCPRJB2nLP2wk+i73yQ5ndWO5T521RXLUlT4E0vLE7Jg+6aoDt3SU4eM=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216</a><br>
</div>
<div><br>
</div>
Since it is crashing there, I think maybe your
manually configured datasets are not matching the
Apollo configuration of the datasets.
<div><br>
</div>
<div>If you make them match up, it might fix it, and
to do that, you may be able to make the dataset ID
be the organism ID that Apollo gives. Would have
to update both the datasets and the dataset_id</div>
<div><br>
</div>
<div>This is where Apollo sets the dataset_id, uses
organism ID <a href="https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440" originalsrc="https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440" shash="jEuwZ0dqegE2z/ek9p2MUYGduI48cfLvBnD+jGpjdItqWKipFg2K5lWfJlacMpQmxUbzuFh1Af2wNKtyYJC01X00kZqfyZCWKPE+AeksUcAS+e1NiEzQvjkT+MBtFW/2MJwV6N5wdBW0/g1FKDERvaIEXSmv/LPeKxeeA0U4Qmo=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440</a><br>
<div><br>
</div>
<div>To be clear, the dataset ID is what is after
the . in the conf format e.g.</div>
<div><br>
</div>
<div>[datasets.make_this_match_the_organismID]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Also, the current generation of Apollo
(Apollo 2) does not work with JBrowse 2, but we
are working on a new Apollo version that will be
integrated with JBrowse 2. It's not ready for
use yet but you can keep an eye on <a href="https://github.com/GMOD/Apollo3" originalsrc="https://github.com/GMOD/Apollo3" shash="ijgN7D+gf4dZ7q0XGy4q02i8BxgPVkel68Ek2TCid0GhO7rem4wYpbfPl7KlLrcrxutD/d8x+jAbIcTYnzSVrlIsow+sbW+aPZoQS4yt7O+bZo/82PzDTbQ8AW1182d9ViNSXVhYu6LHZhSrLC32vNc/GVgpkatSQBe7zIbwWAs=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/Apollo3</a>
if interested</div>
<div><br>
</div>
<div>-Colin</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May 26,
2022 at 9:56 AM Justin Elser <<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>I'm attaching the output from the chrome
console. I don't think it's the non-minified
version of the JS though. How would I get that
with the docker version of apollo?<br>
<br>
Also, I've been asked to ask if Apollo works
with JBrowse2? Would it be better to use that
instead of JBrowse1?<br>
<br>
Thank you for taking the time to help me.<br>
<br>
Justin<br>
<br>
<div>On 5/25/22 4:51 PM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from outside of OSU. Use
caution with links and attachments.]</span></p>
<div>
<div dir="auto">The logs that are probably
most helpful are the "JavaScript console"
or developer console from chrome or
firefox e.g.
<a href="https://balsamiq.com/support/faqs/browserconsole/" originalsrc="https://balsamiq.com/support/faqs/browserconsole/" shash="mQLrKBEXj/KgA6uhAKsooEZXtW49iY/ID1YcURrcIx/erCmYD7Iz4TQ6WrIwcDeS3zSUHzMlJStSEm4pSoK0FQdoamnwLbBEEKYWXC45gFMgyQJfJHl32sVU+9fTJ0VPoOdWsSejvG1eyvvVRhI9s4TqrlkU7KHDDNuNQT9iSLA=" rel="noreferrer" title="Unmangled
Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
https://balsamiq.com/support/faqs/browserconsole/</a></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed,
May 25, 2022, 4:33 PM Justin Elser <<a href="mailto:jus...@or..." rel="noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>We may just use Apollo to serve
both, but thought I might give it a
try to see about JBrowse.<br>
<br>
I am attaching the output I get when I
run the docker container with "-e
WEBAPOLLO_DEBUG=true".<br>
<br>
The blank lines are in between it
working and not working. IE, lines
1-483 are the initial startup and
navigating to the site with Apollo
working as expected. Lines 487 on are
after changing
data/nipponbare/tracks.conf to have:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
I do notice that after the change it
is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
(line 579) where it isn't before. I
don't understand why it would be
looking for the sample data at all. I
never loaded it as a track or
anything.<br>
<br>
I also notice for the initial load
where it works that it is complaining
about the mime_type for .bam files. I
did alter the .htaccess for the
jbrowse but not apollo, so I think
those are fixable and unrelated.
Weirdly enough, the bam track does
load fine in Apollo where it didn't in
JBrowse until I made the change to
.htaccess.<br>
<br>
If you meant some other logs, please
let me know how to get those and I
will send them to you.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22 2:18 PM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from outside of
OSU. Use caution with links and
attachments.]</span></p>
<div>
<div dir="ltr">One option is to
use Apollo to serve your jbrowse
instances, Apollo can serve
public jbrowse instances so you
may not need to configure
jbrowse separately
<div><br>
</div>
<div><br>
<div>If you do want it
separate, then we would
probably need to debug that
error. If you have the stack
trace from the developer
console, it might narrow
down exactly where the error
comes from. If the stack
trace is minified and hard
to read, can possibly use a
"dev" version of jbrowse if
it is too unreadable since
it does not minify the
builds!
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May
25, 2022 at 1:03 PM Justin
Elser <<a href="mailto:jus...@or..." rel="noreferrer noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Yeah, so I guess the
problem is that if I don't
add the "dataset_id" to each
data/(species)/tracks.conf
file, apollo works fine, but
then I can't get the dataset
selector in jbrowse. As I
have it right now, Apollo is
fine, but I have no way to
switch to a different
dataset in JBrowse.<br>
<img alt="" moz-do-not-send="true" width="1073" height="648"><br>
<br>
I was messing around with
jbrowse.conf,
data/tracks.conf, and
data/(species)/tracks.conf,
and was able to get a list
of the species under the
"Genome" tab. But if I don't
have anything in
data/(species)/tracks.conf,
I don't. However, if I do
add it like in the
documentation, the species
are listed under there:<br>
<img alt="" moz-do-not-send="true" width="1021" height="616"><br>
But then, apollo breaks:<br>
<img alt="" moz-do-not-send="true" width="972" height="587"><br>
<br>
So, I guess I need to get
the dataset_selector working
in JBrowse, while not
breaking Apollo.<br>
<br>
I hope that clears it up
more.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22 11:50 AM,
Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from
outside of OSU. Use
caution with links and
attachments.]</span></p>
<div>
<div dir="ltr">
<div>I haven't
evaluated the whole
post here, but note
that Apollo
automatically
creates a dataset
selector from
assemblies that you
configure through
that Apollo
interface</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On
Wed, May 25, 2022 at
12:21 PM Justin
Elser <<a href="mailto:jus...@or..." rel="noreferrer
noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex">
Hi all,<br>
<br>
I have set up a
jbrowse 1.16.11
instance (sorry, not
publicly available)
<br>
and added 2 species
(well, different
cultivars) by doing
the following:<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="B+jVefrKrefTFTkcGlf7AYg0BmqVa9mHbZ5u3RmfVgw9EgDXdiCkXHCajEI4Lygb7aSj1PpKYphvQ/USOKWeUhSfD2nT5VWZGPVTF5P0+y/xPpBU1sLkOBmfsGK2+TaAmrT+UQga0p/nP35BW8Mq1dalvC2r3lUs3/UleGwiOqQ=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
--out
data/nipponbare
--fasta <br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="fjBFMWnFVufXG8eIOm1XK0A0/yYJeqzTnS0Ql/D7wnwq0G7B+0+GOV1/Sb8InKJYF/xc2dFWDlrw2JN/uaOS1dGpnYKCDMYCKQu2E6h3IgFxUSdaPBVlaxssN5AcH412URCrcKYI7bpmvrS6HIgus5UMnBeLjRzI+gHaolCZeF4=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
--out
data/nipponbare
--trackType
CanvasFeatures <br>
--trackLabel MSU7.0
-gff
source_files/MSU7.0.gff3<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="zRCP36TRaHjgLXG5Apd+kvq2QhCT1B4RxEqXILumVcU00nPEo1edu3Lx4Xwc0zzDoQFai54UqYndjmOjL8BpgihHC+u79yKV3Ue5xG0i5LDQdAXIPaPZNICqsYwQHCpj5B/s7KqzwiH6NIUJAyNpgbZ+0/zCR/8PiHN5lEWdy/A=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
--out
data/nipponbare<br>
<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="B+jVefrKrefTFTkcGlf7AYg0BmqVa9mHbZ5u3RmfVgw9EgDXdiCkXHCajEI4Lygb7aSj1PpKYphvQ/USOKWeUhSfD2nT5VWZGPVTF5P0+y/xPpBU1sLkOBmfsGK2+TaAmrT+UQga0p/nP35BW8Mq1dalvC2r3lUs3/UleGwiOqQ=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
--out data/arc
--fasta <br>
source_files/magic_16/oryza_sativa_arc.fa<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="fjBFMWnFVufXG8eIOm1XK0A0/yYJeqzTnS0Ql/D7wnwq0G7B+0+GOV1/Sb8InKJYF/xc2dFWDlrw2JN/uaOS1dGpnYKCDMYCKQu2E6h3IgFxUSdaPBVlaxssN5AcH412URCrcKYI7bpmvrS6HIgus5UMnBeLjRzI+gHaolCZeF4=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
--out data/arc
--trackType
CanvasFeatures <br>
--trackLabel Genes
-gff
source_files/magic_16/oryza_sativa_arc.gff<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="zRCP36TRaHjgLXG5Apd+kvq2QhCT1B4RxEqXILumVcU00nPEo1edu3Lx4Xwc0zzDoQFai54UqYndjmOjL8BpgihHC+u79yKV3Ue5xG0i5LDQdAXIPaPZNICqsYwQHCpj5B/s7KqzwiH6NIUJAyNpgbZ+0/zCR/8PiHN5lEWdy/A=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
--out data/arc<br>
<br>
Then I edited the
jbrowse.conf file as
explained in <br>
<a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="jY79EUL0uW/+K/a6fNnZys8zoiMKyO9tOE4x4BQUcOQm3vxV9gHr/0WYyaQ2I4DhVgua0HTeyR3v6ZBLcVje2jAKG4ny/C2AGUFBmjmAAOjMSvk6XMlH4yglI+9YKOnbsV46xyWJJ+3WbG43nZ6gspE/4txV0LGcHFUJNUfyF80=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
to have:<br>
dataRoot =
data/nipponbare<br>
[datasets.nipponbare]<br>
url =
?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.arc]<br>
url = ?data=data/arc<br>
name = ARC<br>
<br>
And all seems to
work fine, except
that I don't see the
dropdown to <br>
switch datasets, so
I can't actually see
the ARC dataset.
Although I <br>
have by messing
around with
jbrowse.conf and
tracks.conf gotten
it to <br>
work, but at this
point I've left it
out.<br>
<br>
However, the issue
I'm having is
actually with
Apollo. I have the
docker <br>
instance of apollo
running and it seems
to be fine as
configured in a <br>
systemd unit file:<br>
ExecStart=/usr/bin/docker run --rm --name %n \<br>
-e
APOLLO_PATH=apollo \<br>
-v
/data/www/panoryza/jbrowse/<a rel="noreferrer
noreferrer
noreferrer" moz-do-not-send="true">data:/data</a>
\<br>
-v
/data/www/panoryza/apollo/postgres:/var/lib/postgresql
\<br>
-v <br>
/data/www/panoryza/apollo/apollo_<a rel="noreferrer noreferrer
noreferrer" moz-do-not-send="true">data:/data/temporary/apollo_data</a>
\<br>
-p
8887:8080 \<br>
gmod/apollo:latest<br>
<br>
Adding Nipponbare as
an organism with
"Directory"
/data/nipponbare
works <br>
fine and I can see
the tracks I've
added.<br>
<br>
Now, here is where
the issue I have
starts. If I edit
the <br>
data/nipponbare/tracks.conf file as shown in the dataset selector <br>
documentation above:<br>
[general]<br>
dataset_id =
nipponbare<br>
<br>
Apollo then shows
the following error:<br>
Error message(s):<br>
TypeError:
Cannot read
properties of
undefined (reading
'name').<br>
<br>
Clearing out the
data/nipponbare/tracks.conf
file allows apollo
to work.<br>
Now, the error only
appears in apollo,
jbrowse works fine
with the edits.<br>
<br>
I'm a bit confused
about how this
should be configured
to work. I <br>
actually have 14
more "species" to
add, but waiting
till I at least get
<br>
it working with one.
The documentation
isn't clear to me on
the <br>
difference between
adding the datasets
to jbrowse.conf vs <br>
data/tracks.conf vs
data/(species)/tracks.conf.<br>
<br>
Please let me know
if you need any more
information.<br>
<br>
Thanks,<br>
Justin<br>
<br>
-- <br>
**********************************************************<br>
*
*<br>
* Justin Elser
*<br>
* Computational
Biology Research
Associate
*<br>
* Dept. of Botany
and Plant Pathology
*<br>
* Jaiswal Lab
*<br>
* Oregon State
University
*<br>
*
*<br>
* email: <a href="mailto:jus...@or..." rel="noreferrer
noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
jus...@or...</a> *<br>
*
*<br>
**********************************************************<br>
<br>
<br>
<br>
_______________________________________________<br>
Gmod-ajax mailing
list<br>
<a href="mailto:Gmo...@li..." rel="noreferrer
noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="hvejOAKu6wDQj/B3iauaEHuEeOS4V0fQdAWIgA96Z1DMnTavwMpjgwKd5jEOvjO7OEh9Om9L5a+OaBnsZwdCxPy906PRvhsV77hBuKNZtvyvzy4G/V6dy5PsxA8DmsDEnAUyYZFFrkq0vxVAZ9M3Dnn+NR+NrMuDsyBHGhUYjtA=" rel="noreferrer
noreferrer
noreferrer
noreferrer" title="Unmangled
Microsoft
Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a> *
* *
**********************************************************
</pre>
</body>
</html> |
|
From: Colin <col...@gm...> - 2022-06-01 19:29:45
|
Thanks for pointing this out, there was a regression where the fix for this got undone. Will post a fix soon! -Colin On Wed, Jun 1, 2022 at 12:48 PM Ke Jiang <bio...@gm...> wrote: > Hi, > > After upgrading to 1.7.8, this problem seems to be back. In both Firefox > and Safari, the coverage part of the CRAM rendering would give a reload > error: "TypeError: e.bezierCurveTo is not a function". Maybe the "sushimi" > code is not compatible with some recent updates? > > Thanks! > > Ke > > On Fri, Feb 18, 2022 at 3:13 PM Colin <col...@gm...> wrote: > >> Fix released in 1.6.5 :) >> >> Thanks again for reporting! >> >> >> -Colin >> >> On Wed, Feb 16, 2022 at 3:45 PM Colin <col...@gm...> wrote: >> >>> Excellent, thank you for reporting the issue! We should have a new >>> version out soon >>> >>> >>> -Colin >>> >>> On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote: >>> >>>> Hi, Colin, >>>> >>>> Thanks for the quick response. I saw this error with both Safari and >>>> Firefox. Now you mention the rendering issue with the intron lines, I did >>>> notice that a while ago. The distinction between BAM and CRAM mentioned in >>>> the original email was not accurate. The error not showing up for the BAM >>>> tracks was because the coverage was continuous in the WGS data, which >>>> happens to be using BAM, while the RNA-Seq data with introns/gaps happens >>>> to be CRAM files. >>>> >>>> Thank you very much for fixing this! Since it was a small glitch for >>>> alignment tracks only, I think I'll wait for 1.6.5 to upgrade. >>>> >>>> Best. >>>> >>>> Ke >>>> >>>> On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote: >>>> >>>>> Hi Ke, >>>>> This is an interesting error. The issue would probably be related to >>>>> the new rendering of the "sashimi" style arcs introduced in 1.5.2 ( >>>>> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have >>>>> not seen this error. >>>>> >>>>> Can you tell me what browser you are using? >>>>> >>>>> >>>>> I found what I think is a fix here >>>>> https://github.com/GMOD/jbrowse-components/pull/2750 but I would >>>>> still like to know more info because there are also some possible rendering >>>>> glitches in your screenshot (looks like some "intron" lines are drawn on >>>>> top of features). If you have data that reproduces this let me know >>>>> >>>>> >>>>> -Colin >>>>> >>>>> >>>>> >>>>> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> After upgrading to 1.6.4, the CRAM tracks give an error >>>>>> ("e.bezierCurveTo is nor function") when rendering coverage plots (the BAM >>>>>> tracks are fine), the read alignment rendering part seems to be fine. Here >>>>>> is a screenshot and configuration. I'd like to put it here before taking it >>>>>> to github issues, maybe there is a simple fix or configuration error on my >>>>>> side. >>>>>> >>>>>> Thanks! >>>>>> >>>>>> Ke >>>>>> >>>>>> [image: ScreenShot.png] >>>>>> >>>>>> >>>>>> { >>>>>> "type": "AlignmentsTrack", >>>>>> "trackId": "SRR11185046_reads", >>>>>> "name": "SRR11185046", >>>>>> "category": [ >>>>>> "mRNASeq" >>>>>> ], >>>>>> "assemblyNames": [ >>>>>> "Porcine S. scrofa v11.1" >>>>>> ], >>>>>> "adapter": { >>>>>> "type": "CramAdapter", >>>>>> "cramLocation": { >>>>>> "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram" >>>>>> }, >>>>>> "craiLocation": { >>>>>> "uri": >>>>>> "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai" >>>>>> }, >>>>>> "sequenceAdapter": { >>>>>> "type": "IndexedFastaAdapter", >>>>>> "fastaLocation": { >>>>>> "uri": "Sscrofa11.1.fa" >>>>>> }, >>>>>> "faiLocation": { >>>>>> "uri": "Sscrofa11.1.fa.fai" >>>>>> } >>>>>> } >>>>>> } >>>>>> }, >>>>>> _______________________________________________ >>>>>> Gmod-ajax mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>> |
|
From: Ke J. <bio...@gm...> - 2022-06-01 18:49:04
|
Hi, After upgrading to 1.7.8, this problem seems to be back. In both Firefox and Safari, the coverage part of the CRAM rendering would give a reload error: "TypeError: e.bezierCurveTo is not a function". Maybe the "sushimi" code is not compatible with some recent updates? Thanks! Ke On Fri, Feb 18, 2022 at 3:13 PM Colin <col...@gm...> wrote: > Fix released in 1.6.5 :) > > Thanks again for reporting! > > > -Colin > > On Wed, Feb 16, 2022 at 3:45 PM Colin <col...@gm...> wrote: > >> Excellent, thank you for reporting the issue! We should have a new >> version out soon >> >> >> -Colin >> >> On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote: >> >>> Hi, Colin, >>> >>> Thanks for the quick response. I saw this error with both Safari and >>> Firefox. Now you mention the rendering issue with the intron lines, I did >>> notice that a while ago. The distinction between BAM and CRAM mentioned in >>> the original email was not accurate. The error not showing up for the BAM >>> tracks was because the coverage was continuous in the WGS data, which >>> happens to be using BAM, while the RNA-Seq data with introns/gaps happens >>> to be CRAM files. >>> >>> Thank you very much for fixing this! Since it was a small glitch for >>> alignment tracks only, I think I'll wait for 1.6.5 to upgrade. >>> >>> Best. >>> >>> Ke >>> >>> On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote: >>> >>>> Hi Ke, >>>> This is an interesting error. The issue would probably be related to >>>> the new rendering of the "sashimi" style arcs introduced in 1.5.2 ( >>>> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have >>>> not seen this error. >>>> >>>> Can you tell me what browser you are using? >>>> >>>> >>>> I found what I think is a fix here >>>> https://github.com/GMOD/jbrowse-components/pull/2750 but I would still >>>> like to know more info because there are also some possible rendering >>>> glitches in your screenshot (looks like some "intron" lines are drawn on >>>> top of features). If you have data that reproduces this let me know >>>> >>>> >>>> -Colin >>>> >>>> >>>> >>>> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote: >>>> >>>>> Hi, >>>>> >>>>> After upgrading to 1.6.4, the CRAM tracks give an error >>>>> ("e.bezierCurveTo is nor function") when rendering coverage plots (the BAM >>>>> tracks are fine), the read alignment rendering part seems to be fine. Here >>>>> is a screenshot and configuration. I'd like to put it here before taking it >>>>> to github issues, maybe there is a simple fix or configuration error on my >>>>> side. >>>>> >>>>> Thanks! >>>>> >>>>> Ke >>>>> >>>>> [image: ScreenShot.png] >>>>> >>>>> >>>>> { >>>>> "type": "AlignmentsTrack", >>>>> "trackId": "SRR11185046_reads", >>>>> "name": "SRR11185046", >>>>> "category": [ >>>>> "mRNASeq" >>>>> ], >>>>> "assemblyNames": [ >>>>> "Porcine S. scrofa v11.1" >>>>> ], >>>>> "adapter": { >>>>> "type": "CramAdapter", >>>>> "cramLocation": { >>>>> "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram" >>>>> }, >>>>> "craiLocation": { >>>>> "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai" >>>>> }, >>>>> "sequenceAdapter": { >>>>> "type": "IndexedFastaAdapter", >>>>> "fastaLocation": { >>>>> "uri": "Sscrofa11.1.fa" >>>>> }, >>>>> "faiLocation": { >>>>> "uri": "Sscrofa11.1.fa.fai" >>>>> } >>>>> } >>>>> } >>>>> }, >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> |
|
From: Vaneet L. <van...@uc...> - 2022-06-01 17:59:04
|
Hi, I attached a screenshot of the XML parsing errors from the console of my Firefox browser, which I'm a little confused about. I checked the actual configuration files that these errors denote, and I don't see anything wrong or any hidden characters that are there on the first line. I don't think these are file specific though as no matter what genome I switch to in JBrowse I see the same errors, that is those genomes for which I have an extra configuration file for functions that's named 'functions.conf'. The jbrowse.conf error always appears. I don't see any visible problem on the browser tracks that results from these errors but I just want to eliminate them to make sure. After looking at the JBrowse 1 troubleshooting page, I took the suggestion to install the libexpat1-dev package and then rerun the setup.sh script, but errors are still there on Firefox. If I load the page in Microsoft Edge browser, I don't see the errors there, so I'm wondering if it's browser specific? Is anyone aware of any fixes for this specific issue? Thanks, Vaneet |
|
From: Colin <col...@gm...> - 2022-05-26 21:05:46
|
>Everything works as expected now! I see both Nipponbare and ARC in the
"Genome" dropdown, and apollo is showing all data.
Excellent:)
>So, I guess apollo is only using the numeric ID for the dataset instead of
using what I tried to set the dataset id? In other words, if I had
[datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
using it's internal ID of 34?
You can inspect the database for the IDs, or you can get the ID from inside
the URL clicking the link icon, see screenshot attachment here. I don't
think you can change the organism ID to something else like a readable name
unfortunately.
-Colin
On Thu, May 26, 2022 at 12:24 PM Justin Elser <jus...@or...>
wrote:
> Ok, I think I get it. At least, I think I can get it working but I am a
> bit confused.
>
> So, I noticed in the apollo docker logs that I see this:
> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
> apollo.PreferenceService - found organism in session
> org.bbop.apollo.Organism : 34 so returning
> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
> apollo.JbrowseController - got organism org.bbop.apollo.Organism : 34 for
> client token 137967108160676781264638533
> 2022-05-26 18:10:34,649 [http-nio-8080-exec-1] DEBUG
> apollo.AnnotationEditorController - handleOperation annotationEditor
> get_sequence_alterations -> getSequenceAlterations
> 2022-05-26 18:10:34,650 [http-nio-8080-exec-1] DEBUG
> apollo.PermissionService - dataObject does not contain organism (may not
> be needed)
> 2022-05-26 18:10:34,652 [http-nio-8080-exec-1] DEBUG
> apollo.PreferenceService - found in-memory preference:
> {"id":96,"organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"currentOrganism":true,"nativeTrackList":true,"sequence":{"id":36,"name":"chr1","organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"length":43270923,"start":0,"end":43270923},"startbp":6587035,"endbp":7241056,"clientToken":"137967108160676781264638533","user":{"id":32,"username":
> "ad...@lo..." <ad...@lo...>}}
>
> So, it looks like the apollo "id" is 34 for Nipponbare, and similarly 51
> for ARC.
>
> So, I changed the jbrowse.conf to have:
> [datasets.34]
> url = ?data=data/nipponbare
> name = Nipponbare
> [datasets.51]
> url = ?data=data/arc
> name = ARC
> and data/nipponbare/tracks.conf to have:
> [general]
> dataset_id = 34
>
> and similar change for data/arc/tracks.conf.
>
> Everything works as expected now! I see both Nipponbare and ARC in the
> "Genome" dropdown, and apollo is showing all data.
>
> So, I guess apollo is only using the numeric ID for the dataset instead of
> using what I tried to set the dataset id? In other words, if I had
> [datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
> data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
> using it's internal ID of 34?
>
> I guess I just don't understand why apollo isn't seeing the dataset_id I'm
> trying to set in jbrowse instead of seeing it's own ID.
>
> How can I see what ID apollo is going to use without just checking the
> logs and seeing what it looks for? Or can I force it somehow to use
> nipponbare instead of 34?
>
> Thanks for the info on JBrowse2/Apollo3, I'll watch for updates.
>
> Justin
>
> On 5/26/22 11:00 AM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> The code that is crashing is probably this, seeing renderDatasetSelector
> in the stack trace
>
>
> https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216
>
> Since it is crashing there, I think maybe your manually configured
> datasets are not matching the Apollo configuration of the datasets.
>
> If you make them match up, it might fix it, and to do that, you may be
> able to make the dataset ID be the organism ID that Apollo gives. Would
> have to update both the datasets and the dataset_id
>
> This is where Apollo sets the dataset_id, uses organism ID
> https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440
>
> To be clear, the dataset ID is what is after the . in the conf format e.g.
>
> [datasets.make_this_match_the_organismID]
> url = ?data=data/nipponbare
> name = Nipponbare
>
>
> Also, the current generation of Apollo (Apollo 2) does not work with
> JBrowse 2, but we are working on a new Apollo version that will be
> integrated with JBrowse 2. It's not ready for use yet but you can keep an
> eye on https://github.com/GMOD/Apollo3 if interested
>
> -Colin
>
>
>
> On Thu, May 26, 2022 at 9:56 AM Justin Elser <jus...@or...>
> wrote:
>
>> I'm attaching the output from the chrome console. I don't think it's the
>> non-minified version of the JS though. How would I get that with the docker
>> version of apollo?
>>
>> Also, I've been asked to ask if Apollo works with JBrowse2? Would it be
>> better to use that instead of JBrowse1?
>>
>> Thank you for taking the time to help me.
>>
>> Justin
>>
>> On 5/25/22 4:51 PM, Colin wrote:
>>
>> [This email originated from outside of OSU. Use caution with links and
>> attachments.]
>> The logs that are probably most helpful are the "JavaScript console" or
>> developer console from chrome or firefox e.g.
>> https://balsamiq.com/support/faqs/browserconsole/
>>
>> On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...>
>> wrote:
>>
>>> We may just use Apollo to serve both, but thought I might give it a try
>>> to see about JBrowse.
>>>
>>> I am attaching the output I get when I run the docker container with "-e
>>> WEBAPOLLO_DEBUG=true".
>>>
>>> The blank lines are in between it working and not working. IE, lines
>>> 1-483 are the initial startup and navigating to the site with Apollo
>>> working as expected. Lines 487 on are after changing
>>> data/nipponbare/tracks.conf to have:
>>> [general]
>>> dataset_id = nipponbare
>>>
>>> I do notice that after the change it is trying to open
>>> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
>>> (line 579) where it isn't before. I don't understand why it would be
>>> looking for the sample data at all. I never loaded it as a track or
>>> anything.
>>>
>>> I also notice for the initial load where it works that it is complaining
>>> about the mime_type for .bam files. I did alter the .htaccess for the
>>> jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly
>>> enough, the bam track does load fine in Apollo where it didn't in JBrowse
>>> until I made the change to .htaccess.
>>>
>>> If you meant some other logs, please let me know how to get those and I
>>> will send them to you.
>>>
>>> Thanks,
>>> Justin
>>>
>>> On 5/25/22 2:18 PM, Colin wrote:
>>>
>>> [This email originated from outside of OSU. Use caution with links and
>>> attachments.]
>>> One option is to use Apollo to serve your jbrowse instances, Apollo can
>>> serve public jbrowse instances so you may not need to configure jbrowse
>>> separately
>>>
>>>
>>> If you do want it separate, then we would probably need to debug that
>>> error. If you have the stack trace from the developer console, it might
>>> narrow down exactly where the error comes from. If the stack trace is
>>> minified and hard to read, can possibly use a "dev" version of jbrowse if
>>> it is too unreadable since it does not minify the builds!
>>>
>>>
>>>
>>> -Colin
>>>
>>> On Wed, May 25, 2022 at 1:03 PM Justin Elser <
>>> jus...@or...> wrote:
>>>
>>>> Yeah, so I guess the problem is that if I don't add the "dataset_id" to
>>>> each data/(species)/tracks.conf file, apollo works fine, but then I can't
>>>> get the dataset selector in jbrowse. As I have it right now, Apollo is
>>>> fine, but I have no way to switch to a different dataset in JBrowse.
>>>>
>>>>
>>>> I was messing around with jbrowse.conf, data/tracks.conf, and
>>>> data/(species)/tracks.conf, and was able to get a list of the species under
>>>> the "Genome" tab. But if I don't have anything in
>>>> data/(species)/tracks.conf, I don't. However, if I do add it like in the
>>>> documentation, the species are listed under there:
>>>>
>>>> But then, apollo breaks:
>>>>
>>>>
>>>> So, I guess I need to get the dataset_selector working in JBrowse,
>>>> while not breaking Apollo.
>>>>
>>>> I hope that clears it up more.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On 5/25/22 11:50 AM, Colin wrote:
>>>>
>>>> [This email originated from outside of OSU. Use caution with links and
>>>> attachments.]
>>>> I haven't evaluated the whole post here, but note that Apollo
>>>> automatically creates a dataset selector from assemblies that you configure
>>>> through that Apollo interface
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
>>>> jus...@or...> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly
>>>>> available)
>>>>> and added 2 species (well, different cultivars) by doing the following:
>>>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>>>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>>>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType
>>>>> CanvasFeatures
>>>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>>>>> bin/generate-names.pl --out data/nipponbare
>>>>>
>>>>> bin/prepare-refseqs.pl --out data/arc --fasta
>>>>> source_files/magic_16/oryza_sativa_arc.fa
>>>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>>>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>>>>> bin/generate-names.pl --out data/arc
>>>>>
>>>>> Then I edited the jbrowse.conf file as explained in
>>>>> https://jbrowse.org/docs/dataset_selector.html to have:
>>>>> dataRoot = data/nipponbare
>>>>> [datasets.nipponbare]
>>>>> url = ?data=data/nipponbare
>>>>> name = Nipponbare
>>>>> [datasets.arc]
>>>>> url = ?data=data/arc
>>>>> name = ARC
>>>>>
>>>>> And all seems to work fine, except that I don't see the dropdown to
>>>>> switch datasets, so I can't actually see the ARC dataset. Although I
>>>>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>>>>> work, but at this point I've left it out.
>>>>>
>>>>> However, the issue I'm having is actually with Apollo. I have the
>>>>> docker
>>>>> instance of apollo running and it seems to be fine as configured in a
>>>>> systemd unit file:
>>>>> ExecStart=/usr/bin/docker run --rm --name %n \
>>>>> -e APOLLO_PATH=apollo \
>>>>> -v /data/www/panoryza/jbrowse/data:/data \
>>>>> -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>>>> -v
>>>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>>>> -p 8887:8080 \
>>>>> gmod/apollo:latest
>>>>>
>>>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare
>>>>> works
>>>>> fine and I can see the tracks I've added.
>>>>>
>>>>> Now, here is where the issue I have starts. If I edit the
>>>>> data/nipponbare/tracks.conf file as shown in the dataset selector
>>>>> documentation above:
>>>>> [general]
>>>>> dataset_id = nipponbare
>>>>>
>>>>> Apollo then shows the following error:
>>>>> Error message(s):
>>>>> TypeError: Cannot read properties of undefined (reading 'name').
>>>>>
>>>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to
>>>>> work.
>>>>> Now, the error only appears in apollo, jbrowse works fine with the
>>>>> edits.
>>>>>
>>>>> I'm a bit confused about how this should be configured to work. I
>>>>> actually have 14 more "species" to add, but waiting till I at least
>>>>> get
>>>>> it working with one. The documentation isn't clear to me on the
>>>>> difference between adding the datasets to jbrowse.conf vs
>>>>> data/tracks.conf vs data/(species)/tracks.conf.
>>>>>
>>>>> Please let me know if you need any more information.
>>>>>
>>>>> Thanks,
>>>>> Justin
>>>>>
>>>>> --
>>>>> **********************************************************
>>>>> * *
>>>>> * Justin Elser *
>>>>> * Computational Biology Research Associate *
>>>>> * Dept. of Botany and Plant Pathology *
>>>>> * Jaiswal Lab *
>>>>> * Oregon State University *
>>>>> * *
>>>>> * email: jus...@or... *
>>>>> * *
>>>>> **********************************************************
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>>> --
>>>> **********************************************************
>>>> * *
>>>> * Justin Elser *
>>>> * Computational Biology Research Associate *
>>>> * Dept. of Botany and Plant Pathology *
>>>> * Jaiswal Lab *
>>>> * Oregon State University *
>>>> * *
>>>> * email: jus...@or... *
>>>> * *
>>>> **********************************************************
>>>>
>>>>
>>> --
>>> **********************************************************
>>> * *
>>> * Justin Elser *
>>> * Computational Biology Research Associate *
>>> * Dept. of Botany and Plant Pathology *
>>> * Jaiswal Lab *
>>> * Oregon State University *
>>> * *
>>> * email: jus...@or... *
>>> * *
>>> **********************************************************
>>>
>>>
>> --
>> **********************************************************
>> * *
>> * Justin Elser *
>> * Computational Biology Research Associate *
>> * Dept. of Botany and Plant Pathology *
>> * Jaiswal Lab *
>> * Oregon State University *
>> * *
>> * email: jus...@or... *
>> * *
>> **********************************************************
>>
>>
> --
> **********************************************************
> * *
> * Justin Elser *
> * Computational Biology Research Associate *
> * Dept. of Botany and Plant Pathology *
> * Jaiswal Lab *
> * Oregon State University *
> * *
> * email: jus...@or... *
> * *
> **********************************************************
>
>
|
|
From: Colin <col...@gm...> - 2022-05-26 18:00:58
|
The code that is crashing is probably this, seeing renderDatasetSelector in the stack trace https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216 Since it is crashing there, I think maybe your manually configured datasets are not matching the Apollo configuration of the datasets. If you make them match up, it might fix it, and to do that, you may be able to make the dataset ID be the organism ID that Apollo gives. Would have to update both the datasets and the dataset_id This is where Apollo sets the dataset_id, uses organism ID https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440 To be clear, the dataset ID is what is after the . in the conf format e.g. [datasets.make_this_match_the_organismID] url = ?data=data/nipponbare name = Nipponbare Also, the current generation of Apollo (Apollo 2) does not work with JBrowse 2, but we are working on a new Apollo version that will be integrated with JBrowse 2. It's not ready for use yet but you can keep an eye on https://github.com/GMOD/Apollo3 if interested -Colin On Thu, May 26, 2022 at 9:56 AM Justin Elser <jus...@or...> wrote: > I'm attaching the output from the chrome console. I don't think it's the > non-minified version of the JS though. How would I get that with the docker > version of apollo? > > Also, I've been asked to ask if Apollo works with JBrowse2? Would it be > better to use that instead of JBrowse1? > > Thank you for taking the time to help me. > > Justin > > On 5/25/22 4:51 PM, Colin wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > The logs that are probably most helpful are the "JavaScript console" or > developer console from chrome or firefox e.g. > https://balsamiq.com/support/faqs/browserconsole/ > > On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...> > wrote: > >> We may just use Apollo to serve both, but thought I might give it a try >> to see about JBrowse. >> >> I am attaching the output I get when I run the docker container with "-e >> WEBAPOLLO_DEBUG=true". >> >> The blank lines are in between it working and not working. IE, lines >> 1-483 are the initial startup and navigating to the site with Apollo >> working as expected. Lines 487 on are after changing >> data/nipponbare/tracks.conf to have: >> [general] >> dataset_id = nipponbare >> >> I do notice that after the change it is trying to open >> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run >> (line 579) where it isn't before. I don't understand why it would be >> looking for the sample data at all. I never loaded it as a track or >> anything. >> >> I also notice for the initial load where it works that it is complaining >> about the mime_type for .bam files. I did alter the .htaccess for the >> jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly >> enough, the bam track does load fine in Apollo where it didn't in JBrowse >> until I made the change to .htaccess. >> >> If you meant some other logs, please let me know how to get those and I >> will send them to you. >> >> Thanks, >> Justin >> >> On 5/25/22 2:18 PM, Colin wrote: >> >> [This email originated from outside of OSU. Use caution with links and >> attachments.] >> One option is to use Apollo to serve your jbrowse instances, Apollo can >> serve public jbrowse instances so you may not need to configure jbrowse >> separately >> >> >> If you do want it separate, then we would probably need to debug that >> error. If you have the stack trace from the developer console, it might >> narrow down exactly where the error comes from. If the stack trace is >> minified and hard to read, can possibly use a "dev" version of jbrowse if >> it is too unreadable since it does not minify the builds! >> >> >> >> -Colin >> >> On Wed, May 25, 2022 at 1:03 PM Justin Elser < >> jus...@or...> wrote: >> >>> Yeah, so I guess the problem is that if I don't add the "dataset_id" to >>> each data/(species)/tracks.conf file, apollo works fine, but then I can't >>> get the dataset selector in jbrowse. As I have it right now, Apollo is >>> fine, but I have no way to switch to a different dataset in JBrowse. >>> >>> >>> I was messing around with jbrowse.conf, data/tracks.conf, and >>> data/(species)/tracks.conf, and was able to get a list of the species under >>> the "Genome" tab. But if I don't have anything in >>> data/(species)/tracks.conf, I don't. However, if I do add it like in the >>> documentation, the species are listed under there: >>> >>> But then, apollo breaks: >>> >>> >>> So, I guess I need to get the dataset_selector working in JBrowse, while >>> not breaking Apollo. >>> >>> I hope that clears it up more. >>> >>> Thanks, >>> Justin >>> >>> On 5/25/22 11:50 AM, Colin wrote: >>> >>> [This email originated from outside of OSU. Use caution with links and >>> attachments.] >>> I haven't evaluated the whole post here, but note that Apollo >>> automatically creates a dataset selector from assemblies that you configure >>> through that Apollo interface >>> >>> >>> -Colin >>> >>> On Wed, May 25, 2022 at 12:21 PM Justin Elser < >>> jus...@or...> wrote: >>> >>>> Hi all, >>>> >>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly >>>> available) >>>> and added 2 species (well, different cultivars) by doing the following: >>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta >>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta >>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType >>>> CanvasFeatures >>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3 >>>> bin/generate-names.pl --out data/nipponbare >>>> >>>> bin/prepare-refseqs.pl --out data/arc --fasta >>>> source_files/magic_16/oryza_sativa_arc.fa >>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures >>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff >>>> bin/generate-names.pl --out data/arc >>>> >>>> Then I edited the jbrowse.conf file as explained in >>>> https://jbrowse.org/docs/dataset_selector.html to have: >>>> dataRoot = data/nipponbare >>>> [datasets.nipponbare] >>>> url = ?data=data/nipponbare >>>> name = Nipponbare >>>> [datasets.arc] >>>> url = ?data=data/arc >>>> name = ARC >>>> >>>> And all seems to work fine, except that I don't see the dropdown to >>>> switch datasets, so I can't actually see the ARC dataset. Although I >>>> have by messing around with jbrowse.conf and tracks.conf gotten it to >>>> work, but at this point I've left it out. >>>> >>>> However, the issue I'm having is actually with Apollo. I have the >>>> docker >>>> instance of apollo running and it seems to be fine as configured in a >>>> systemd unit file: >>>> ExecStart=/usr/bin/docker run --rm --name %n \ >>>> -e APOLLO_PATH=apollo \ >>>> -v /data/www/panoryza/jbrowse/data:/data \ >>>> -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \ >>>> -v >>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \ >>>> -p 8887:8080 \ >>>> gmod/apollo:latest >>>> >>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare >>>> works >>>> fine and I can see the tracks I've added. >>>> >>>> Now, here is where the issue I have starts. If I edit the >>>> data/nipponbare/tracks.conf file as shown in the dataset selector >>>> documentation above: >>>> [general] >>>> dataset_id = nipponbare >>>> >>>> Apollo then shows the following error: >>>> Error message(s): >>>> TypeError: Cannot read properties of undefined (reading 'name'). >>>> >>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to work. >>>> Now, the error only appears in apollo, jbrowse works fine with the >>>> edits. >>>> >>>> I'm a bit confused about how this should be configured to work. I >>>> actually have 14 more "species" to add, but waiting till I at least get >>>> it working with one. The documentation isn't clear to me on the >>>> difference between adding the datasets to jbrowse.conf vs >>>> data/tracks.conf vs data/(species)/tracks.conf. >>>> >>>> Please let me know if you need any more information. >>>> >>>> Thanks, >>>> Justin >>>> >>>> -- >>>> ********************************************************** >>>> * * >>>> * Justin Elser * >>>> * Computational Biology Research Associate * >>>> * Dept. of Botany and Plant Pathology * >>>> * Jaiswal Lab * >>>> * Oregon State University * >>>> * * >>>> * email: jus...@or... * >>>> * * >>>> ********************************************************** >>>> >>>> >>>> >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> >>> -- >>> ********************************************************** >>> * * >>> * Justin Elser * >>> * Computational Biology Research Associate * >>> * Dept. of Botany and Plant Pathology * >>> * Jaiswal Lab * >>> * Oregon State University * >>> * * >>> * email: jus...@or... * >>> * * >>> ********************************************************** >>> >>> >> -- >> ********************************************************** >> * * >> * Justin Elser * >> * Computational Biology Research Associate * >> * Dept. of Botany and Plant Pathology * >> * Jaiswal Lab * >> * Oregon State University * >> * * >> * email: jus...@or... * >> * * >> ********************************************************** >> >> > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Research Associate * > * Dept. of Botany and Plant Pathology * > * Jaiswal Lab * > * Oregon State University * > * * > * email: jus...@or... * > * * > ********************************************************** > > |
|
From: Justin E. <jus...@or...> - 2022-05-26 16:12:00
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
I'm attaching the output from the chrome console. I don't think it's
the non-minified version of the JS though. How would I get that with
the docker version of apollo?<br>
<br>
Also, I've been asked to ask if Apollo works with JBrowse2? Would it
be better to use that instead of JBrowse1?<br>
<br>
Thank you for taking the time to help me.<br>
<br>
Justin<br>
<br>
<div class="moz-cite-prefix">On 5/25/22 4:51 PM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+...@ma...">
<p><span style="color:#D73F09;">[This email originated from
outside of OSU. Use caution with links and attachments.]</span></p>
<div>
<div dir="auto">The logs that are probably most helpful are the
"JavaScript console" or developer console from chrome or
firefox e.g.
<a href="https://balsamiq.com/support/faqs/browserconsole/" originalsrc="https://balsamiq.com/support/faqs/browserconsole/" shash="aiCz/OnBddYj4od+LOHVXj9Tq5GlWP+IORJqZ7Z7WBgj41oQOhE6mVZWYKNq3E0Kyx93xXSRfQlDQXIRn5/3DI65xgWOCgmuM3HVWxzEAMEGHi4BHvsGl+pzPy81lK3hZKdsSpdeB1zr1lRpwLktCpwpuC3PzjKbGTSE8dJWgcc=" target="_blank" rel="noreferrer" moz-do-not-send="true" title="Unmangled Microsoft Safelink" class="moz-txt-link-freetext">
https://balsamiq.com/support/faqs/browserconsole/</a></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 25, 2022, 4:33
PM Justin Elser <<a href="mailto:jus...@or..." rel="noreferrer
noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>We may just use Apollo to serve both, but thought I
might give it a try to see about JBrowse.<br>
<br>
I am attaching the output I get when I run the docker
container with "-e WEBAPOLLO_DEBUG=true".<br>
<br>
The blank lines are in between it working and not working.
IE, lines 1-483 are the initial startup and navigating to
the site with Apollo working as expected. Lines 487 on are
after changing data/nipponbare/tracks.conf to have:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
I do notice that after the change it is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
(line 579) where it isn't before. I don't understand why
it would be looking for the sample data at all. I never
loaded it as a track or anything.<br>
<br>
I also notice for the initial load where it works that it
is complaining about the mime_type for .bam files. I did
alter the .htaccess for the jbrowse but not apollo, so I
think those are fixable and unrelated. Weirdly enough, the
bam track does load fine in Apollo where it didn't in
JBrowse until I made the change to .htaccess.<br>
<br>
If you meant some other logs, please let me know how to
get those and I will send them to you.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22 2:18 PM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:#d73f09">[This email originated
from outside of OSU. Use caution with links and
attachments.]</span></p>
<div>
<div dir="ltr">One option is to use Apollo to serve
your jbrowse instances, Apollo can serve public
jbrowse instances so you may not need to configure
jbrowse separately
<div><br>
</div>
<div><br>
<div>If you do want it separate, then we would
probably need to debug that error. If you have
the stack trace from the developer console, it
might narrow down exactly where the error comes
from. If the stack trace is minified and hard to
read, can possibly use a "dev" version of
jbrowse if it is too unreadable since it does
not minify the builds!
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 25,
2022 at 1:03 PM Justin Elser <<a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Yeah, so I guess the problem is that if I
don't add the "dataset_id" to each
data/(species)/tracks.conf file, apollo works
fine, but then I can't get the dataset selector
in jbrowse. As I have it right now, Apollo is
fine, but I have no way to switch to a different
dataset in JBrowse.<br>
<img src="cid:par...@or..." alt="" moz-do-not-send="true" width="1073" height="648"><br>
<br>
I was messing around with jbrowse.conf,
data/tracks.conf, and
data/(species)/tracks.conf, and was able to get
a list of the species under the "Genome" tab.
But if I don't have anything in
data/(species)/tracks.conf, I don't. However, if
I do add it like in the documentation, the
species are listed under there:<br>
<img src="cid:par...@or..." alt="" moz-do-not-send="true" width="1021" height="616"><br>
But then, apollo breaks:<br>
<img src="cid:par...@or..." alt="" moz-do-not-send="true" width="972" height="587"><br>
<br>
So, I guess I need to get the dataset_selector
working in JBrowse, while not breaking Apollo.<br>
<br>
I hope that clears it up more.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22 11:50 AM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from outside of OSU. Use
caution with links and attachments.]</span></p>
<div>
<div dir="ltr">
<div>I haven't evaluated the whole post
here, but note that Apollo automatically
creates a dataset selector from
assemblies that you configure through
that Apollo interface</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed,
May 25, 2022 at 12:21 PM Justin Elser
<<a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Hi all,<br>
<br>
I have set up a jbrowse 1.16.11 instance
(sorry, not publicly available) <br>
and added 2 species (well, different
cultivars) by doing the following:<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="Iw7JIv8JSxSDakGiUb5b42Bd55gBvCt4+3TQJyt6NutlLU290Wx2IqOWIp5gDEiGUWJaCBDjpEfGozPb6ncagFq1AHUOlM7nQs4lIgTBhtQCE7h5xMQzIJoW92/4pX6pqzDclcxOWbatbmh27zPetOrxtomFvDrLnVinn1BiQF0=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
--out data/nipponbare --fasta
<br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="djDv4cv/Q25cSdu8YcftqlGVE9DKJD0CIceloNveCO+o3AZubjfgaJteYEMhTJY1uT2bNR4NfoGYeM48i4H3LVQGHF1yzA/ZVnbYkSq1hDOP0V5p8yh9YYgREocd9Dm+n1MRZPQre0W+h3jISY+H+GyN2UQT/z362L6QsXdATX0=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
--out data/nipponbare --trackType
CanvasFeatures
<br>
--trackLabel MSU7.0 -gff
source_files/MSU7.0.gff3<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="BozVmS4CdIphHrkpb9yb93YpWCD3ohMCi6uO2tznjLcnGqXfLhC2sjK6H+90f/pxP5+JjAPJbv48hEq0weXBVMj6Ptirgrof7VWV7y2r/G9gqFcjrO9HD4HzG3ZIG4aH4gnPv/3ji8eyWlbdLGbi/taDo6hyU+YFcHEC9XOjB4g=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
--out data/nipponbare<br>
<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="Iw7JIv8JSxSDakGiUb5b42Bd55gBvCt4+3TQJyt6NutlLU290Wx2IqOWIp5gDEiGUWJaCBDjpEfGozPb6ncagFq1AHUOlM7nQs4lIgTBhtQCE7h5xMQzIJoW92/4pX6pqzDclcxOWbatbmh27zPetOrxtomFvDrLnVinn1BiQF0=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
--out data/arc --fasta
<br>
source_files/magic_16/oryza_sativa_arc.fa<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="djDv4cv/Q25cSdu8YcftqlGVE9DKJD0CIceloNveCO+o3AZubjfgaJteYEMhTJY1uT2bNR4NfoGYeM48i4H3LVQGHF1yzA/ZVnbYkSq1hDOP0V5p8yh9YYgREocd9Dm+n1MRZPQre0W+h3jISY+H+GyN2UQT/z362L6QsXdATX0=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
--out data/arc --trackType
CanvasFeatures
<br>
--trackLabel Genes -gff
source_files/magic_16/oryza_sativa_arc.gff<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="BozVmS4CdIphHrkpb9yb93YpWCD3ohMCi6uO2tznjLcnGqXfLhC2sjK6H+90f/pxP5+JjAPJbv48hEq0weXBVMj6Ptirgrof7VWV7y2r/G9gqFcjrO9HD4HzG3ZIG4aH4gnPv/3ji8eyWlbdLGbi/taDo6hyU+YFcHEC9XOjB4g=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
--out data/arc<br>
<br>
Then I edited the jbrowse.conf file as
explained in <br>
<a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="I/Hc19jvjhytQo9VcQEUMphArpjSAzZBLWbP00xLK8q30977hYU+iIG5ukzKihOT6O6pqoYRHWBrKDzosuVSIzmA3fbT0Cru7PW/nHQpXYaltwuftgI7YChftu+aNs3y6RNiacz+6Zc+jKe8yXJ0Ddqetw+Ptuv7NsWIs6udSpY=" rel="noreferrer noreferrer noreferrer
noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
to have:<br>
dataRoot = data/nipponbare<br>
[datasets.nipponbare]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.arc]<br>
url = ?data=data/arc<br>
name = ARC<br>
<br>
And all seems to work fine, except that
I don't see the dropdown to <br>
switch datasets, so I can't actually see
the ARC dataset. Although I <br>
have by messing around with jbrowse.conf
and tracks.conf gotten it to <br>
work, but at this point I've left it
out.<br>
<br>
However, the issue I'm having is
actually with Apollo. I have the docker
<br>
instance of apollo running and it seems
to be fine as configured in a <br>
systemd unit file:<br>
ExecStart=/usr/bin/docker run --rm
--name %n \<br>
-e APOLLO_PATH=apollo \<br>
-v /data/www/panoryza/jbrowse/<a rel="noreferrer noreferrer noreferrer" moz-do-not-send="true">data:/data</a>
\<br>
-v
/data/www/panoryza/apollo/postgres:/var/lib/postgresql
\<br>
-v <br>
/data/www/panoryza/apollo/apollo_<a rel="noreferrer noreferrer noreferrer" moz-do-not-send="true">data:/data/temporary/apollo_data</a>
\<br>
-p 8887:8080 \<br>
gmod/apollo:latest<br>
<br>
Adding Nipponbare as an organism with
"Directory" /data/nipponbare works <br>
fine and I can see the tracks I've
added.<br>
<br>
Now, here is where the issue I have
starts. If I edit the <br>
data/nipponbare/tracks.conf file as
shown in the dataset selector <br>
documentation above:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
Apollo then shows the following error:<br>
Error message(s):<br>
TypeError: Cannot read properties
of undefined (reading 'name').<br>
<br>
Clearing out the
data/nipponbare/tracks.conf file allows
apollo to work.<br>
Now, the error only appears in apollo,
jbrowse works fine with the edits.<br>
<br>
I'm a bit confused about how this should
be configured to work. I <br>
actually have 14 more "species" to add,
but waiting till I at least get <br>
it working with one. The documentation
isn't clear to me on the <br>
difference between adding the datasets
to jbrowse.conf vs <br>
data/tracks.conf vs
data/(species)/tracks.conf.<br>
<br>
Please let me know if you need any more
information.<br>
<br>
Thanks,<br>
Justin<br>
<br>
-- <br>
**********************************************************<br>
*
*<br>
* Justin Elser
*<br>
* Computational Biology Research
Associate *<br>
* Dept. of Botany and Plant Pathology
*<br>
* Jaiswal Lab
*<br>
* Oregon State University
*<br>
*
*<br>
* email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
jus...@or...</a>
*<br>
*
*<br>
**********************************************************<br>
<br>
<br>
<br>
_______________________________________________<br>
Gmod-ajax mailing list<br>
<a href="mailto:Gmo...@li..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
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</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a> *
* *
**********************************************************
</pre>
</body>
</html> |
|
From: Justin E. <jus...@or...> - 2022-05-26 01:07:42
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
We may just use Apollo to serve both, but thought I might give it a
try to see about JBrowse.<br>
<br>
I am attaching the output I get when I run the docker container with
"-e WEBAPOLLO_DEBUG=true".<br>
<br>
The blank lines are in between it working and not working. IE, lines
1-483 are the initial startup and navigating to the site with Apollo
working as expected. Lines 487 on are after changing
data/nipponbare/tracks.conf to have:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
I do notice that after the change it is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
(line 579) where it isn't before. I don't understand why it would be
looking for the sample data at all. I never loaded it as a track or
anything.<br>
<br>
I also notice for the initial load where it works that it is
complaining about the mime_type for .bam files. I did alter the
.htaccess for the jbrowse but not apollo, so I think those are
fixable and unrelated. Weirdly enough, the bam track does load fine
in Apollo where it didn't in JBrowse until I made the change to
.htaccess.<br>
<br>
If you meant some other logs, please let me know how to get those
and I will send them to you.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div class="moz-cite-prefix">On 5/25/22 2:18 PM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+...@ma...">
<p><span style="color:#D73F09;">[This email originated from
outside of OSU. Use caution with links and attachments.]</span></p>
<div>
<div dir="ltr">One option is to use Apollo to serve your jbrowse
instances, Apollo can serve public jbrowse instances so you
may not need to configure jbrowse separately
<div><br>
</div>
<div><br>
<div>If you do want it separate, then we would probably need
to debug that error. If you have the stack trace from the
developer console, it might narrow down exactly where the
error comes from. If the stack trace is minified and hard
to read, can possibly use a "dev" version of jbrowse if it
is too unreadable since it does not minify the builds!
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 25, 2022 at 1:03
PM Justin Elser <<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Yeah, so I guess the problem is that if I don't add the
"dataset_id" to each data/(species)/tracks.conf file,
apollo works fine, but then I can't get the dataset
selector in jbrowse. As I have it right now, Apollo is
fine, but I have no way to switch to a different dataset
in JBrowse.<br>
<img src="cid:par...@or..." alt="" class="" width="1073" height="648"><br>
<br>
I was messing around with jbrowse.conf, data/tracks.conf,
and data/(species)/tracks.conf, and was able to get a list
of the species under the "Genome" tab. But if I don't have
anything in data/(species)/tracks.conf, I don't. However,
if I do add it like in the documentation, the species are
listed under there:<br>
<img src="cid:par...@or..." alt="" class="" width="1021" height="616"><br>
But then, apollo breaks:<br>
<img src="cid:par...@or..." alt="" class="" width="972" height="587"><br>
<br>
So, I guess I need to get the dataset_selector working in
JBrowse, while not breaking Apollo.<br>
<br>
I hope that clears it up more.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 5/25/22 11:50 AM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This email
originated from outside of OSU. Use caution with
links and attachments.]</span></p>
<div>
<div dir="ltr">
<div>I haven't evaluated the whole post here, but
note that Apollo automatically creates a dataset
selector from assemblies that you configure
through that Apollo interface</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 25,
2022 at 12:21 PM Justin Elser <<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Hi all,<br>
<br>
I have set up a jbrowse 1.16.11 instance (sorry,
not publicly available) <br>
and added 2 species (well, different cultivars) by
doing the following:<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="uWeJJjB9s93rzDNTEzCi3RakZCyt4ux/WC2ZoqKcYa1rGzS6R/h8TMuA3cBa8U1hWeK2PmNrobskt3PS6tzO83xSvYt7rTv1SbgQnAxOhm7gKfMpvabsYcnM1d34DS/QRKdyV+1JgHuKhc3KX5vyw/MDw8lj80BKnGa/HEkKbwk=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
--out data/nipponbare --fasta
<br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="zKgfqQ8d6GV9SwADCBr1AuH+GzqREPTQ0IUT6KnLEGvLVN3OQBJEeXN0sj8J1BZ/Whw7CCTB3nzTFpFzurhKINO7cCc2gSnW6mGCwzlrajwbjAjJWd/Nr8u4TgNfCMXlUCvDU6DOUN35UhFScB531PcpYc1w/t/TMQVeRxqfc6w=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
--out data/nipponbare --trackType CanvasFeatures
<br>
--trackLabel MSU7.0 -gff source_files/MSU7.0.gff3<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="AEsH1IjqM6NIi/IjuCY9OYb3R61LcMr+v40tJyq7GMpxdq0bFveddo2JRQoOUXs7Arkhb+jU9rw/xgeHNuAAw4ZfZrJ3WBIFKBNKLZcL6QtpeM16HJ8MOM9on5gPe7b3mewTLmJRcnUe+15HWEhZ+D5VCKN/MJfT80eVGKWeNYI=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
--out data/nipponbare<br>
<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="uWeJJjB9s93rzDNTEzCi3RakZCyt4ux/WC2ZoqKcYa1rGzS6R/h8TMuA3cBa8U1hWeK2PmNrobskt3PS6tzO83xSvYt7rTv1SbgQnAxOhm7gKfMpvabsYcnM1d34DS/QRKdyV+1JgHuKhc3KX5vyw/MDw8lj80BKnGa/HEkKbwk=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
--out data/arc --fasta
<br>
source_files/magic_16/oryza_sativa_arc.fa<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="zKgfqQ8d6GV9SwADCBr1AuH+GzqREPTQ0IUT6KnLEGvLVN3OQBJEeXN0sj8J1BZ/Whw7CCTB3nzTFpFzurhKINO7cCc2gSnW6mGCwzlrajwbjAjJWd/Nr8u4TgNfCMXlUCvDU6DOUN35UhFScB531PcpYc1w/t/TMQVeRxqfc6w=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
--out data/arc --trackType CanvasFeatures
<br>
--trackLabel Genes -gff
source_files/magic_16/oryza_sativa_arc.gff<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="AEsH1IjqM6NIi/IjuCY9OYb3R61LcMr+v40tJyq7GMpxdq0bFveddo2JRQoOUXs7Arkhb+jU9rw/xgeHNuAAw4ZfZrJ3WBIFKBNKLZcL6QtpeM16HJ8MOM9on5gPe7b3mewTLmJRcnUe+15HWEhZ+D5VCKN/MJfT80eVGKWeNYI=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
--out data/arc<br>
<br>
Then I edited the jbrowse.conf file as explained
in <br>
<a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="iTq9PpsQjfikWqhtGN7FCNRL57lgYKDKZzWc2TrzkiLKGUpqxn9A0TDQXbFwduJIfFcnzVaq3EPIiFw1fq504i6ZkF5ZYUVYuY4wX8IQ5vlk2nTXXBhYAbhx2olcMjrkYqC9+w9yTvpjRuewl+pJ9I5fMW5LUsH7pNqhziooqYs=" rel="noreferrer" title="Unmangled Microsoft
Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
to have:<br>
dataRoot = data/nipponbare<br>
[datasets.nipponbare]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.arc]<br>
url = ?data=data/arc<br>
name = ARC<br>
<br>
And all seems to work fine, except that I don't
see the dropdown to <br>
switch datasets, so I can't actually see the ARC
dataset. Although I <br>
have by messing around with jbrowse.conf and
tracks.conf gotten it to <br>
work, but at this point I've left it out.<br>
<br>
However, the issue I'm having is actually with
Apollo. I have the docker <br>
instance of apollo running and it seems to be fine
as configured in a <br>
systemd unit file:<br>
ExecStart=/usr/bin/docker run --rm --name %n \<br>
-e APOLLO_PATH=apollo \<br>
-v /data/www/panoryza/jbrowse/<a moz-do-not-send="true">data:/data</a> \<br>
-v
/data/www/panoryza/apollo/postgres:/var/lib/postgresql
\<br>
-v <br>
/data/www/panoryza/apollo/apollo_<a moz-do-not-send="true">data:/data/temporary/apollo_data</a>
\<br>
-p 8887:8080 \<br>
gmod/apollo:latest<br>
<br>
Adding Nipponbare as an organism with "Directory"
/data/nipponbare works <br>
fine and I can see the tracks I've added.<br>
<br>
Now, here is where the issue I have starts. If I
edit the <br>
data/nipponbare/tracks.conf file as shown in the
dataset selector <br>
documentation above:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
Apollo then shows the following error:<br>
Error message(s):<br>
TypeError: Cannot read properties of
undefined (reading 'name').<br>
<br>
Clearing out the data/nipponbare/tracks.conf file
allows apollo to work.<br>
Now, the error only appears in apollo, jbrowse
works fine with the edits.<br>
<br>
I'm a bit confused about how this should be
configured to work. I <br>
actually have 14 more "species" to add, but
waiting till I at least get <br>
it working with one. The documentation isn't clear
to me on the <br>
difference between adding the datasets to
jbrowse.conf vs <br>
data/tracks.conf vs data/(species)/tracks.conf.<br>
<br>
Please let me know if you need any more
information.<br>
<br>
Thanks,<br>
Justin<br>
<br>
-- <br>
**********************************************************<br>
*
*<br>
* Justin Elser
*<br>
* Computational Biology Research Associate
*<br>
* Dept. of Botany and Plant Pathology
*<br>
* Jaiswal Lab
*<br>
* Oregon State University
*<br>
*
*<br>
* email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>
*<br>
*
*<br>
**********************************************************<br>
<br>
<br>
<br>
_______________________________________________<br>
Gmod-ajax mailing list<br>
<a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
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Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a> *
* *
**********************************************************
</pre>
</body>
</html> |
|
From: Colin <col...@gm...> - 2022-05-25 23:52:14
|
The logs that are probably most helpful are the "JavaScript console" or developer console from chrome or firefox e.g. https://balsamiq.com/support/faqs/browserconsole/ On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...> wrote: > We may just use Apollo to serve both, but thought I might give it a try to > see about JBrowse. > > I am attaching the output I get when I run the docker container with "-e > WEBAPOLLO_DEBUG=true". > > The blank lines are in between it working and not working. IE, lines 1-483 > are the initial startup and navigating to the site with Apollo working as > expected. Lines 487 on are after changing data/nipponbare/tracks.conf to > have: > [general] > dataset_id = nipponbare > > I do notice that after the change it is trying to open > /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run > (line 579) where it isn't before. I don't understand why it would be > looking for the sample data at all. I never loaded it as a track or > anything. > > I also notice for the initial load where it works that it is complaining > about the mime_type for .bam files. I did alter the .htaccess for the > jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly > enough, the bam track does load fine in Apollo where it didn't in JBrowse > until I made the change to .htaccess. > > If you meant some other logs, please let me know how to get those and I > will send them to you. > > Thanks, > Justin > > On 5/25/22 2:18 PM, Colin wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > One option is to use Apollo to serve your jbrowse instances, Apollo can > serve public jbrowse instances so you may not need to configure jbrowse > separately > > > If you do want it separate, then we would probably need to debug that > error. If you have the stack trace from the developer console, it might > narrow down exactly where the error comes from. If the stack trace is > minified and hard to read, can possibly use a "dev" version of jbrowse if > it is too unreadable since it does not minify the builds! > > > > -Colin > > On Wed, May 25, 2022 at 1:03 PM Justin Elser <jus...@or...> > wrote: > >> Yeah, so I guess the problem is that if I don't add the "dataset_id" to >> each data/(species)/tracks.conf file, apollo works fine, but then I can't >> get the dataset selector in jbrowse. As I have it right now, Apollo is >> fine, but I have no way to switch to a different dataset in JBrowse. >> >> >> I was messing around with jbrowse.conf, data/tracks.conf, and >> data/(species)/tracks.conf, and was able to get a list of the species under >> the "Genome" tab. But if I don't have anything in >> data/(species)/tracks.conf, I don't. However, if I do add it like in the >> documentation, the species are listed under there: >> >> But then, apollo breaks: >> >> >> So, I guess I need to get the dataset_selector working in JBrowse, while >> not breaking Apollo. >> >> I hope that clears it up more. >> >> Thanks, >> Justin >> >> On 5/25/22 11:50 AM, Colin wrote: >> >> [This email originated from outside of OSU. Use caution with links and >> attachments.] >> I haven't evaluated the whole post here, but note that Apollo >> automatically creates a dataset selector from assemblies that you configure >> through that Apollo interface >> >> >> -Colin >> >> On Wed, May 25, 2022 at 12:21 PM Justin Elser < >> jus...@or...> wrote: >> >>> Hi all, >>> >>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly available) >>> and added 2 species (well, different cultivars) by doing the following: >>> bin/prepare-refseqs.pl --out data/nipponbare --fasta >>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta >>> bin/flatfile-to-json.pl --out data/nipponbare --trackType >>> CanvasFeatures >>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3 >>> bin/generate-names.pl --out data/nipponbare >>> >>> bin/prepare-refseqs.pl --out data/arc --fasta >>> source_files/magic_16/oryza_sativa_arc.fa >>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures >>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff >>> bin/generate-names.pl --out data/arc >>> >>> Then I edited the jbrowse.conf file as explained in >>> https://jbrowse.org/docs/dataset_selector.html to have: >>> dataRoot = data/nipponbare >>> [datasets.nipponbare] >>> url = ?data=data/nipponbare >>> name = Nipponbare >>> [datasets.arc] >>> url = ?data=data/arc >>> name = ARC >>> >>> And all seems to work fine, except that I don't see the dropdown to >>> switch datasets, so I can't actually see the ARC dataset. Although I >>> have by messing around with jbrowse.conf and tracks.conf gotten it to >>> work, but at this point I've left it out. >>> >>> However, the issue I'm having is actually with Apollo. I have the docker >>> instance of apollo running and it seems to be fine as configured in a >>> systemd unit file: >>> ExecStart=/usr/bin/docker run --rm --name %n \ >>> -e APOLLO_PATH=apollo \ >>> -v /data/www/panoryza/jbrowse/data:/data \ >>> -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \ >>> -v >>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \ >>> -p 8887:8080 \ >>> gmod/apollo:latest >>> >>> Adding Nipponbare as an organism with "Directory" /data/nipponbare works >>> fine and I can see the tracks I've added. >>> >>> Now, here is where the issue I have starts. If I edit the >>> data/nipponbare/tracks.conf file as shown in the dataset selector >>> documentation above: >>> [general] >>> dataset_id = nipponbare >>> >>> Apollo then shows the following error: >>> Error message(s): >>> TypeError: Cannot read properties of undefined (reading 'name'). >>> >>> Clearing out the data/nipponbare/tracks.conf file allows apollo to work. >>> Now, the error only appears in apollo, jbrowse works fine with the edits. >>> >>> I'm a bit confused about how this should be configured to work. I >>> actually have 14 more "species" to add, but waiting till I at least get >>> it working with one. The documentation isn't clear to me on the >>> difference between adding the datasets to jbrowse.conf vs >>> data/tracks.conf vs data/(species)/tracks.conf. >>> >>> Please let me know if you need any more information. >>> >>> Thanks, >>> Justin >>> >>> -- >>> ********************************************************** >>> * * >>> * Justin Elser * >>> * Computational Biology Research Associate * >>> * Dept. of Botany and Plant Pathology * >>> * Jaiswal Lab * >>> * Oregon State University * >>> * * >>> * email: jus...@or... * >>> * * >>> ********************************************************** >>> >>> >>> >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> >> -- >> ********************************************************** >> * * >> * Justin Elser * >> * Computational Biology Research Associate * >> * Dept. of Botany and Plant Pathology * >> * Jaiswal Lab * >> * Oregon State University * >> * * >> * email: jus...@or... * >> * * >> ********************************************************** >> >> > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Research Associate * > * Dept. of Botany and Plant Pathology * > * Jaiswal Lab * > * Oregon State University * > * * > * email: jus...@or... * > * * > ********************************************************** > > |
|
From: Colin <col...@gm...> - 2022-05-25 21:18:57
|
One option is to use Apollo to serve your jbrowse instances, Apollo can serve public jbrowse instances so you may not need to configure jbrowse separately If you do want it separate, then we would probably need to debug that error. If you have the stack trace from the developer console, it might narrow down exactly where the error comes from. If the stack trace is minified and hard to read, can possibly use a "dev" version of jbrowse if it is too unreadable since it does not minify the builds! -Colin On Wed, May 25, 2022 at 1:03 PM Justin Elser <jus...@or...> wrote: > Yeah, so I guess the problem is that if I don't add the "dataset_id" to > each data/(species)/tracks.conf file, apollo works fine, but then I can't > get the dataset selector in jbrowse. As I have it right now, Apollo is > fine, but I have no way to switch to a different dataset in JBrowse. > > > I was messing around with jbrowse.conf, data/tracks.conf, and > data/(species)/tracks.conf, and was able to get a list of the species under > the "Genome" tab. But if I don't have anything in > data/(species)/tracks.conf, I don't. However, if I do add it like in the > documentation, the species are listed under there: > > But then, apollo breaks: > > > So, I guess I need to get the dataset_selector working in JBrowse, while > not breaking Apollo. > > I hope that clears it up more. > > Thanks, > Justin > > On 5/25/22 11:50 AM, Colin wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > I haven't evaluated the whole post here, but note that Apollo > automatically creates a dataset selector from assemblies that you configure > through that Apollo interface > > > -Colin > > On Wed, May 25, 2022 at 12:21 PM Justin Elser < > jus...@or...> wrote: > >> Hi all, >> >> I have set up a jbrowse 1.16.11 instance (sorry, not publicly available) >> and added 2 species (well, different cultivars) by doing the following: >> bin/prepare-refseqs.pl --out data/nipponbare --fasta >> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta >> bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures >> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3 >> bin/generate-names.pl --out data/nipponbare >> >> bin/prepare-refseqs.pl --out data/arc --fasta >> source_files/magic_16/oryza_sativa_arc.fa >> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures >> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff >> bin/generate-names.pl --out data/arc >> >> Then I edited the jbrowse.conf file as explained in >> https://jbrowse.org/docs/dataset_selector.html to have: >> dataRoot = data/nipponbare >> [datasets.nipponbare] >> url = ?data=data/nipponbare >> name = Nipponbare >> [datasets.arc] >> url = ?data=data/arc >> name = ARC >> >> And all seems to work fine, except that I don't see the dropdown to >> switch datasets, so I can't actually see the ARC dataset. Although I >> have by messing around with jbrowse.conf and tracks.conf gotten it to >> work, but at this point I've left it out. >> >> However, the issue I'm having is actually with Apollo. I have the docker >> instance of apollo running and it seems to be fine as configured in a >> systemd unit file: >> ExecStart=/usr/bin/docker run --rm --name %n \ >> -e APOLLO_PATH=apollo \ >> -v /data/www/panoryza/jbrowse/data:/data \ >> -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \ >> -v >> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \ >> -p 8887:8080 \ >> gmod/apollo:latest >> >> Adding Nipponbare as an organism with "Directory" /data/nipponbare works >> fine and I can see the tracks I've added. >> >> Now, here is where the issue I have starts. If I edit the >> data/nipponbare/tracks.conf file as shown in the dataset selector >> documentation above: >> [general] >> dataset_id = nipponbare >> >> Apollo then shows the following error: >> Error message(s): >> TypeError: Cannot read properties of undefined (reading 'name'). >> >> Clearing out the data/nipponbare/tracks.conf file allows apollo to work. >> Now, the error only appears in apollo, jbrowse works fine with the edits. >> >> I'm a bit confused about how this should be configured to work. I >> actually have 14 more "species" to add, but waiting till I at least get >> it working with one. The documentation isn't clear to me on the >> difference between adding the datasets to jbrowse.conf vs >> data/tracks.conf vs data/(species)/tracks.conf. >> >> Please let me know if you need any more information. >> >> Thanks, >> Justin >> >> -- >> ********************************************************** >> * * >> * Justin Elser * >> * Computational Biology Research Associate * >> * Dept. of Botany and Plant Pathology * >> * Jaiswal Lab * >> * Oregon State University * >> * * >> * email: jus...@or... * >> * * >> ********************************************************** >> >> >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Research Associate * > * Dept. of Botany and Plant Pathology * > * Jaiswal Lab * > * Oregon State University * > * * > * email: jus...@or... * > * * > ********************************************************** > > |
|
From: Justin E. <jus...@or...> - 2022-05-25 20:37:55
|
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<body>
Yeah, so I guess the problem is that if I don't add the "dataset_id"
to each data/(species)/tracks.conf file, apollo works fine, but then
I can't get the dataset selector in jbrowse. As I have it right now,
Apollo is fine, but I have no way to switch to a different dataset
in JBrowse.<br>
<img src="cid:par...@or..." alt="" width="1073" height="648"><br>
<br>
I was messing around with jbrowse.conf, data/tracks.conf, and
data/(species)/tracks.conf, and was able to get a list of the
species under the "Genome" tab. But if I don't have anything in
data/(species)/tracks.conf, I don't. However, if I do add it like in
the documentation, the species are listed under there:<br>
<img src="cid:par...@or..." alt="" width="1021" height="616"><br>
But then, apollo breaks:<br>
<img src="cid:par...@or..." alt="" width="972" height="587"><br>
<br>
So, I guess I need to get the dataset_selector working in JBrowse,
while not breaking Apollo.<br>
<br>
I hope that clears it up more.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div class="moz-cite-prefix">On 5/25/22 11:50 AM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+...@ma...">
<p><span style="color:#D73F09;">[This email originated from
outside of OSU. Use caution with links and attachments.]</span></p>
<div>
<div dir="ltr">
<div>I haven't evaluated the whole post here, but note that
Apollo automatically creates a dataset selector from
assemblies that you configure through that Apollo interface</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div>-Colin</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, May 25, 2022 at
12:21 PM Justin Elser <<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Hi all,<br>
<br>
I have set up a jbrowse 1.16.11 instance (sorry, not
publicly available) <br>
and added 2 species (well, different cultivars) by doing the
following:<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="vDZg07JxIpNJ9SgJzz2LwjbWbu8SZAiokVgcdDRj6LUgO6iAMhYwW9Z0FIXdB5UtpFCd8QZr6rEERKDxgPH2e0Ce9zF2mnoTCJR7X9AdyU5lhWNpvjgxOdixxU6R4+74IQmdEOmb04yVM89miQnoEc/JygeEmooSw18QFFvfdW4=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">prepare-refseqs.pl</a>
--out data/nipponbare --fasta
<br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="jz4oaK2Wo/C+nxugXiV44jGiRLNVPLRJfJryV/FsZWPhUZV+IYb1pvz92/AWbU+u3PUDNN8/G/N6Cwm8enn0OYBQn6cpy8WqsLts/2aWjxm3+bLCz+9iF5tayFpWacmHXEi4xH8rwGZHYdSh0fHbCWVzgB70NW+yXrS9gcUpn7Y=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">flatfile-to-json.pl</a>
--out data/nipponbare --trackType CanvasFeatures
<br>
--trackLabel MSU7.0 -gff source_files/MSU7.0.gff3<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="TsXMi6c3CubeCT8PiCe0pyMle3yjX2ZziNDXE4nXnX8sfBIiqA5ma1QZSf0NeGul85lIAyVU30OuJs2bcs8NjeHw56utqne7+ELMoWBQTUF9zcdEyN3nuqvReN7OyvazMClcqtPxIjZBGEegA8Psod2d2hYxjJ8WuQVlHB57LyY=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">generate-names.pl</a>
--out data/nipponbare<br>
<br>
bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="vDZg07JxIpNJ9SgJzz2LwjbWbu8SZAiokVgcdDRj6LUgO6iAMhYwW9Z0FIXdB5UtpFCd8QZr6rEERKDxgPH2e0Ce9zF2mnoTCJR7X9AdyU5lhWNpvjgxOdixxU6R4+74IQmdEOmb04yVM89miQnoEc/JygeEmooSw18QFFvfdW4=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">prepare-refseqs.pl</a>
--out data/arc --fasta
<br>
source_files/magic_16/oryza_sativa_arc.fa<br>
bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="vWccfMWLvZwkIbe4x7F6sdOJGPKKVxaaBtExf9G4aS8kXEwkgZczQ42oy341GccmCCj6fg7IVTE3tz+bX+jeKzhnCEO0rwD1nMpBGz5Jvxl/xSy3ZlE4ddlZ89plKxnGIsfo2jWC8EmcL3sJgGNLU7SqC6ZyDi4R4uR6yIY8ub0=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">flatfile-to-json.pl</a>
--out data/arc --trackType CanvasFeatures
<br>
--trackLabel Genes -gff
source_files/magic_16/oryza_sativa_arc.gff<br>
bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="lH56QhD00nWxUgDDOxKhXeL6CA6BS+gRwqKHZgDCdToe1e+3Vdeo81Iv9fNyjQFecc/d1WQ994kfGApGN89fCDMnx/eghC4t1s6pYzvAp0HfCouryb6mB45fL3s+GmhVhm5Vf0CDxGlMZQGcpezRYayo9e6B0jJBiNR0Pc/HOaY=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">generate-names.pl</a>
--out data/arc<br>
<br>
Then I edited the jbrowse.conf file as explained in <br>
<a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="TNt2K6nKz3VtRTClTdZhLEyShTUc4ZraZlvMeeMoUF8lUY6IdV/F//7+nviwFOXfPTwjlXcpU9jenaatyJynMD285YAxD5658VNkwcK8UzugOvxgQ6KyKl1VOOdGFspTk2W4KK5svCk7clykEtDbRFwJy9Lin2+zmc0vaiRSByI=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
to have:<br>
dataRoot = data/nipponbare<br>
[datasets.nipponbare]<br>
url = ?data=data/nipponbare<br>
name = Nipponbare<br>
[datasets.arc]<br>
url = ?data=data/arc<br>
name = ARC<br>
<br>
And all seems to work fine, except that I don't see the
dropdown to <br>
switch datasets, so I can't actually see the ARC dataset.
Although I <br>
have by messing around with jbrowse.conf and tracks.conf
gotten it to <br>
work, but at this point I've left it out.<br>
<br>
However, the issue I'm having is actually with Apollo. I
have the docker <br>
instance of apollo running and it seems to be fine as
configured in a <br>
systemd unit file:<br>
ExecStart=/usr/bin/docker run --rm --name %n \<br>
-e APOLLO_PATH=apollo \<br>
-v /data/www/panoryza/jbrowse/<a class="moz-txt-link-freetext" href="data:/data">data:/data</a> \<br>
-v
/data/www/panoryza/apollo/postgres:/var/lib/postgresql \<br>
-v <br>
/data/www/panoryza/apollo/apollo_<a class="moz-txt-link-freetext" href="data:/data/temporary/apollo_data">data:/data/temporary/apollo_data</a> \<br>
-p 8887:8080 \<br>
gmod/apollo:latest<br>
<br>
Adding Nipponbare as an organism with "Directory"
/data/nipponbare works <br>
fine and I can see the tracks I've added.<br>
<br>
Now, here is where the issue I have starts. If I edit the <br>
data/nipponbare/tracks.conf file as shown in the dataset
selector <br>
documentation above:<br>
[general]<br>
dataset_id = nipponbare<br>
<br>
Apollo then shows the following error:<br>
Error message(s):<br>
TypeError: Cannot read properties of undefined (reading
'name').<br>
<br>
Clearing out the data/nipponbare/tracks.conf file allows
apollo to work.<br>
Now, the error only appears in apollo, jbrowse works fine
with the edits.<br>
<br>
I'm a bit confused about how this should be configured to
work. I <br>
actually have 14 more "species" to add, but waiting till I
at least get <br>
it working with one. The documentation isn't clear to me on
the <br>
difference between adding the datasets to jbrowse.conf vs <br>
data/tracks.conf vs data/(species)/tracks.conf.<br>
<br>
Please let me know if you need any more information.<br>
<br>
Thanks,<br>
Justin<br>
<br>
-- <br>
**********************************************************<br>
* *<br>
* Justin Elser *<br>
* Computational Biology Research Associate *<br>
* Dept. of Botany and Plant Pathology *<br>
* Jaiswal Lab *<br>
* Oregon State University *<br>
* *<br>
* email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>
*<br>
* *<br>
**********************************************************<br>
<br>
<br>
<br>
_______________________________________________<br>
Gmod-ajax mailing list<br>
<a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="GbwbWEy14gGDziZJSrKQhQTAWjCJGyUG5PhtseEVugNFLO7L/k5oeGae4eFUHCbsFXhMt9VQPGHQLR+hWGekfUHsewAHeSHxu1CfvmCUE8szi2i+Yo/SdeFrCdTw2t2Iu+FXXWp20BNo0MJR44jsp1YtLdt2CeeOWk6Vt2GXEgM=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Research Associate *
* Dept. of Botany and Plant Pathology *
* Jaiswal Lab *
* Oregon State University *
* *
* email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a> *
* *
**********************************************************
</pre>
</body>
</html> |
|
From: Colin <col...@gm...> - 2022-05-25 18:50:28
|
I haven't evaluated the whole post here, but note that Apollo automatically creates a dataset selector from assemblies that you configure through that Apollo interface -Colin On Wed, May 25, 2022 at 12:21 PM Justin Elser <jus...@or...> wrote: > Hi all, > > I have set up a jbrowse 1.16.11 instance (sorry, not publicly available) > and added 2 species (well, different cultivars) by doing the following: > bin/prepare-refseqs.pl --out data/nipponbare --fasta > source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta > bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures > --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3 > bin/generate-names.pl --out data/nipponbare > > bin/prepare-refseqs.pl --out data/arc --fasta > source_files/magic_16/oryza_sativa_arc.fa > bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures > --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff > bin/generate-names.pl --out data/arc > > Then I edited the jbrowse.conf file as explained in > https://jbrowse.org/docs/dataset_selector.html to have: > dataRoot = data/nipponbare > [datasets.nipponbare] > url = ?data=data/nipponbare > name = Nipponbare > [datasets.arc] > url = ?data=data/arc > name = ARC > > And all seems to work fine, except that I don't see the dropdown to > switch datasets, so I can't actually see the ARC dataset. Although I > have by messing around with jbrowse.conf and tracks.conf gotten it to > work, but at this point I've left it out. > > However, the issue I'm having is actually with Apollo. I have the docker > instance of apollo running and it seems to be fine as configured in a > systemd unit file: > ExecStart=/usr/bin/docker run --rm --name %n \ > -e APOLLO_PATH=apollo \ > -v /data/www/panoryza/jbrowse/data:/data \ > -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \ > -v > /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \ > -p 8887:8080 \ > gmod/apollo:latest > > Adding Nipponbare as an organism with "Directory" /data/nipponbare works > fine and I can see the tracks I've added. > > Now, here is where the issue I have starts. If I edit the > data/nipponbare/tracks.conf file as shown in the dataset selector > documentation above: > [general] > dataset_id = nipponbare > > Apollo then shows the following error: > Error message(s): > TypeError: Cannot read properties of undefined (reading 'name'). > > Clearing out the data/nipponbare/tracks.conf file allows apollo to work. > Now, the error only appears in apollo, jbrowse works fine with the edits. > > I'm a bit confused about how this should be configured to work. I > actually have 14 more "species" to add, but waiting till I at least get > it working with one. The documentation isn't clear to me on the > difference between adding the datasets to jbrowse.conf vs > data/tracks.conf vs data/(species)/tracks.conf. > > Please let me know if you need any more information. > > Thanks, > Justin > > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Research Associate * > * Dept. of Botany and Plant Pathology * > * Jaiswal Lab * > * Oregon State University * > * * > * email: jus...@or... * > * * > ********************************************************** > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Justin E. <jus...@or...> - 2022-05-25 18:21:43
|
Hi all, I have set up a jbrowse 1.16.11 instance (sorry, not publicly available) and added 2 species (well, different cultivars) by doing the following: bin/prepare-refseqs.pl --out data/nipponbare --fasta source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3 bin/generate-names.pl --out data/nipponbare bin/prepare-refseqs.pl --out data/arc --fasta source_files/magic_16/oryza_sativa_arc.fa bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff bin/generate-names.pl --out data/arc Then I edited the jbrowse.conf file as explained in https://jbrowse.org/docs/dataset_selector.html to have: dataRoot = data/nipponbare [datasets.nipponbare] url = ?data=data/nipponbare name = Nipponbare [datasets.arc] url = ?data=data/arc name = ARC And all seems to work fine, except that I don't see the dropdown to switch datasets, so I can't actually see the ARC dataset. Although I have by messing around with jbrowse.conf and tracks.conf gotten it to work, but at this point I've left it out. However, the issue I'm having is actually with Apollo. I have the docker instance of apollo running and it seems to be fine as configured in a systemd unit file: ExecStart=/usr/bin/docker run --rm --name %n \ -e APOLLO_PATH=apollo \ -v /data/www/panoryza/jbrowse/data:/data \ -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \ -v /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \ -p 8887:8080 \ gmod/apollo:latest Adding Nipponbare as an organism with "Directory" /data/nipponbare works fine and I can see the tracks I've added. Now, here is where the issue I have starts. If I edit the data/nipponbare/tracks.conf file as shown in the dataset selector documentation above: [general] dataset_id = nipponbare Apollo then shows the following error: Error message(s): TypeError: Cannot read properties of undefined (reading 'name'). Clearing out the data/nipponbare/tracks.conf file allows apollo to work. Now, the error only appears in apollo, jbrowse works fine with the edits. I'm a bit confused about how this should be configured to work. I actually have 14 more "species" to add, but waiting till I at least get it working with one. The documentation isn't clear to me on the difference between adding the datasets to jbrowse.conf vs data/tracks.conf vs data/(species)/tracks.conf. Please let me know if you need any more information. Thanks, Justin -- ********************************************************** * * * Justin Elser * * Computational Biology Research Associate * * Dept. of Botany and Plant Pathology * * Jaiswal Lab * * Oregon State University * * * * email: jus...@or... * * * ********************************************************** |
|
From: Colin <col...@gm...> - 2022-05-23 19:15:38
|
Thanks for reporting, Mm10 is a default genome that we ship in JBrowse 2 desktop, but we have not fleshed it out as a resource and it does not yet have a gene track or gene names indexed We can definitely add this to our todo list! -Colin On Mon, May 23, 2022 at 12:18 PM Scott Cain <sc...@sc...> wrote: > Please keep the JBrowse mailing list looped in, since more eyes==more > chance of finding the problem! > > Is this in the desktop application or the webserved JBrowse? Can you send > a jbrowse.conf file (which you would have if it's a web application)? > Troubleshooting the desktop application might be a little harder, but I > imagine there is a problem configuring the search index. If you're using > the desktop version, can you send a screenshot of the configuration window > around configuring search for the mouse genome? > > On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote: > >> I test on my laptop. Yes, i am not able to put a gene name into the box >> instead only coordinate. >> No problem when using the human genome. >> >> >> ------------------------------ >> *From:* Scott Cain <sc...@sc...> >> *Sent:* Monday, May 23, 2022 1:36 PM >> *To:* Chang, Hsi <xz...@iu...> >> *Cc:* gmo...@li... <gmo...@li...> >> *Subject:* [External] Re: [Gmod-ajax] Inquiry >> >> You don't often get email from sc...@sc.... Learn why this is >> important <https://aka.ms/LearnAboutSenderIdentification> >> This message was sent from a non-IU address. Please exercise caution when >> clicking links or opening attachments from external sources. >> >> Hi, >> >> Can you give us a little more information? Is this in a publicly >> available JBrowse instance? Can you give us a URL? When you write "Select >> the region", are you searching for something and it isn't working? >> >> Thanks, >> Scott >> >> >> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote: >> >> I don't know I am not available select the region based on the gene for >> mm10 genome, but the hg38 working fine. >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Bq%2Fwh73pfSEYBt29cXIR%2FppkANRsJiZFbCuV98s1AYU%3D&reserved=0> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott >> at scottcain dot net >> GMOD Project Manager (http://gmod.org/ >> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TGrhbM9qtF1qANq%2F9jQ7juSMrJKjFWwelG1Vcb%2F8%2BtI%3D&reserved=0>) >> 216-392-3087 >> WormBase Developer (http://wormbase.org/ >> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pC2HWkICiEhNwc9Vl7%2BSZ7N3JfLnrgR%2BbMTwsc5d6gQ%3D&reserved=0> >> ) >> Alliance of Genome Resources Group Leader (http://alliancegenome.org/ >> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ioi6znKFbZr7CPoHJlS%2BcaeX19PLfQBrZ37KAa08Hmk%3D&reserved=0> >> ) >> VirusSeq Project Manager (https://virusseq-dataportal.ca/ >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CeX5FLeaGH0Z9dqgyKPNdMTbANKQLAYYAQy6axbN5cU%3D&reserved=0> >> ) >> Human Cancer Models Initiative Project Manager ( >> https://hcmi-searchable-catalog.nci.nih.gov/ >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3x3PoXwVkWvCg3nGaSHSRSaEH82%2BiM3Ph4Q7DuIORms%3D&reserved=0> >> ) >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott > at scottcain dot net > GMOD Project Manager (http://gmod.org/) > 216-392-3087 > WormBase Developer (http://wormbase.org/) > Alliance of Genome Resources Group Leader (http://alliancegenome.org/) > VirusSeq Project Manager (https://virusseq-dataportal.ca/) > Human Cancer Models Initiative Project Manager ( > https://hcmi-searchable-catalog.nci.nih.gov/) > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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