Hi Galaxy,
I'm trying to put one of my java tool in galaxy.
I've copied the required files in my tool directory under /tools/jvarkit
(I can see it galaxy)
$ ls
commons-jexl-2.1.1.jar
commons-logging-1.1.1.jar
htsjdk-1.129.jar
snappy-java-1.0.3-rc3.jar
vcffilterjs.jar
vcffilterjs.xml
Here is the content of vcffilterjs.xml
<?xml version="1.0"?>
<tool hidden="false"
id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS"
version="1.0.0" name="vcffilterjs">
<requirements>
<requirement type="binary">java</requirement>
</requirements>
<command><![CDATA[java -cp
$INSTALL_DIR/commons-jexl-2.1.1.jar:$INSTALL_DIR/commons-logging-1.1.1.jar:$INSTALL_DIR/htsjdk-1.129.jar:$INSTALL_DIR/snappy-java-1.0.3-rc3.jar:$INSTALL_DIR/vcffilterjs.jar
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
'${expression}' -o ${output} ${input} 2> /tmp/error ]]></command>
<inputs>
<param format="vcf" name="input" type="data" label="VCF input"/>
<param name="expression" type="text" label="javascript
expression"/>
</inputs>
<outputs>
<data format="vcf" name="output"/>
</outputs>
<stdio>
<exit_code range="1:"/>
<exit_code range=":-1"/>
</stdio>
<help>(...)</help>
</tool>
When I run this tool, the log says:
NotFound: cannot find 'INSTALL_DIR'
If I replace $INSTALL_DIR with \$INSTALL_DIR , the error on stderr is :
Error: Could not find or load main class
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
How can I make this work ?
Bonus question: is there a way to catch the error file to display it in
galaxy when a process fails ?
Thanks;
Pierre
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