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Re: [Gmod-ajax] Dataset selector in apollo
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From: Justin E. <jus...@or...> - 2022-06-01 21:04:55
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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+ZENaJDHxrgizJpUHoBND2OKstw3p957qjzJtBUnCU=WNPT=g...@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:admin@local.host" target="_blank" moz-do-not-send="true">"admin@local.host"</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>
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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 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>
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