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Re: [Gmod-ajax] Dataset selector in apollo
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From: Justin E. <jus...@or...> - 2022-05-26 01:07:42
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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>
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</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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