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implementing requested changes -- dockerhub->quay, versioning image, adding output, suppressing stderr for green history item

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This commit is contained in:
Luke Sargent
2021-03-04 14:54:00 -08:00
parent 0fc14952bd
commit de3092483d
1 changed files with 8 additions and 9 deletions
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tools/interactive/interactivetool_bam_iobio.xml
+8 -9
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@@ -1,6 +1,6 @@
<tool id="interactive_tool_bam_iobio" tool_type="interactive" name="bam.iobio visualisation" version="0.2">
<requirements>
<container type="docker">anderspitman/bam.iobio.io:latest</container>
<container type="docker">quay.io/iobio/bam.iobio.io:0.3.0</container>
</requirements>
<entry_points>
<entry_point name="BAM io.bio visualisation of $baminfile.display_name" requires_domain="True">
@@ -12,19 +12,20 @@
#import re
mkdir -p /bam/input_files;
#set $bam_cleaned_name = re.sub('[^\w\-\.]', '_', str($baminfile.element_identifier))
#set $bai_cleaned_name = re.sub('[^\w\-\.]', '_', str($baiinfile.element_identifier))
ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' &&
ln -sf '$baiinfile' '/bam/input_files/${bai_cleaned_name}' &&
echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bai_cleaned_name}"}' >> /bam/config/config.json &&
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 &
node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam;
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="baminfile" type="data" format="bam" label="BAM file"/>
<param name="baiinfile" type="data" format="bai" label="BAI file"/>
</inputs>
<outputs>
<data name="outfile" format="txt" />
</outputs>
<tests>
</tests>
<help>
@@ -32,8 +33,6 @@
1. BAM file: binary alignment map file
2. BAI file: corresponding index file
The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.
.. _iobio project: https://iobio.io