Menu
▾
▴
Re: [Gmod-ajax] Dataset selector in apollo
|
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>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="EPnrKpyvEtw7mAGHbeofol6OgROlyD2hqBp2Rvfgxo8sVXbT1DHMZzsuDOe+dVPgpobqDHHASWyoEnV2KXog53/ndTG1hwUjHk1BVJ94rKaUsnzLPBDzF0S5PloX/Tx8QTQSMo+fb3meY+KpcWlZuthmbavp2Gb/RU7gix9oosc=" 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 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> |
