opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #11537 from luke-c-sargent/dev

Browse Source 
Update bam.iobio interactive tool wrapper
This commit is contained in:
Marius van den Beek
2021-09-08 13:14:53 +02:00
committed by GitHub
parent 4344a9c781 66c7508186
commit 04885b4ae2
1 changed files with 24 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/interactive/interactivetool_bam_iobio.xml
+24 -28
View File
@@ -1,39 +1,27 @@
<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="BAM (iobio) Visualisation" version="0.1">
<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.4.0">
<requirements>
<container type="docker">qiaoy/iobio-bundle.bam-iobio:1.0-ondemand</container>
<container type="docker">quay.io/iobio/bam.iobio.io:0.4.0</container>
</requirements>
<entry_points>
<entry_point name="BAM io.bio visualisation of $infile.display_name" requires_domain="True">
<port>80</port>
<url><![CDATA[/?bam=http://localhost/tmp/bamfile.bam&region=1]]></url>
<entry_point name="BAM io.bio visualisation of $baminfile.element_identifier" requires_domain="True">
<port>9001</port>
<url>/</url>
</entry_point>
</entry_points>
<command><![CDATA[
## ToDo: websocket could not be found
## WebSocket connection to 'ws://localhost/bamreaddepther/' failed: Error in connection establishment: net::ERR_CONNECTION_REFUSED
#set $PUB_HOSTNAME = 'localhost'
#set $PUB_HTTP_PORT = '80'
cd /var/www/html &&
sed -i "s@\"wss://services.iobio.io/samtools/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samtools/\"@" js/bam.iobio.js/bam.iobio.js &&
sed -i "s@\"wss://services.iobio.io/bamreaddepther/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamreaddepther/\"@" js/bam.iobio.js/bam.iobio.js &&
sed -i "s@\"wss://services.iobio.io/bamstatsalive/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/bamstatsalive/\"@" js/bam.iobio.js/bam.iobio.js &&
sed -i "s@\"wss://services.iobio.io/samheader/\"@((window.location.protocol === \"https:\") ? \"wss://\" : \"ws://\") + window.location.host + \"/samheader/\"@" js/bam.iobio.js/bam.iobio.js &&
sed -i 's/deny all;//g' /etc/nginx/nginx.conf &&
cp '${infile}' /input/bamfile.bam &&
cp '${infile.metadata.bam_index}' /input/bamfile.bam.bai &&
mkdir /var/log/supervisor/ &&
head -n -2 /etc/supervisor.d/app.conf > /tmp/app.conf &&
mv /tmp/app.conf /etc/supervisor.d/app.conf &&
/usr/bin/supervisord -c /etc/supervisord.conf
#import re
mkdir -p /bam/input_files;
#set $bam_cleaned_name = re.sub('[^\w\-\.]', '_', str($baminfile.element_identifier))
ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' &&
ln -sf '$baminfile.metadata.bam_index' '/bam/input_files/${bam_cleaned_name}.bai' &&
echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bam_cleaned_name}.bai"}' >> /bam/config/config.json &&
cd /bam/input_files &&
node /iobio-gru-backend/src/static_server.js 9999 > /dev/null 2>&1 &
node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam > /dev/null 2>&1;
]]>
</command>
<inputs>
<param name="infile" type="data" format="bam" label="BAM file"/>
<param name="baminfile" type="data" format="bam" label="BAM file"/>
</inputs>
<outputs>
<data name="outfile" format="txt" />
@@ -41,6 +29,14 @@
<tests>
</tests>
<help>
BAM iobio visualisation.
Required inputs:
1. BAM file: binary alignment map file
The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.
.. _iobio project: https://iobio.io
.. _Marth lab: https://marthlab.org/
.. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/
</help>
</tool>