On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum
<pierre.lindenb...@univ-nantes.fr> wrote:
> Hi Peter,
>
>
> i wrote the tool_dependencies.xml
>
>
>    <?xml version="1.0"?>
>    <tool_dependency>
>         <package name="jvarkit" version="1.0.0">
>             <install version="1.0.0">
>                 <actions>
>                     <action type="set_environment">
>                         <environment_variable name="JVARKITDIR"
>    action="set_to">$INSTALL_DIR</environment_variable>
>                     </action>
>                 </actions>
>             </install>
>             <readme></readme>
>         </package>
>    </tool_dependency>
>
>
>
>
> and updated vcffilterjs.xml
>
>
>    <?xml version="1.0"?>
>    <tool hidden="false"
>    id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS"
>    version="1.0.0" name="vcffilterjs">
>       <requirements>
>           <requirement type="package" version="1.0.0">jvarkit</requirement>
>         <requirement type="binary">java</requirement>
>       </requirements>
>
>
>       <command><![CDATA[java -cp
>
> \$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar
>    com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
>    '${expression}' -o ${output} ${input}  ]]></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>
>
>
>
> I still get an error:

Could you confirm if the environment variable is being set now?

> (...)
>
>    :24,289 (31) command is: java -cp
> $JVARKITDIR/commons-jexl-2.1.1.jar:$JVARKITDIR/commons-logging-1.1.1.jar:$JVARKITDIR/htsjdk-1.129.jar:$JVARKITDIR/snappy-java-1.0.3-rc3.jar:$JVARKITDIR/vcffilterjs.jar
> com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e 'variant!=nullX'
> -o
> /home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_27.dat
> /home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_1.dat;
> return_code=$?; c
> (...)
> galaxy.jobs DEBUG 2015-02-26 13:31:24,333 (31) Persisting job destination
> (destination id: local:///)
> galaxy.jobs.runners.local DEBUG 2015-02-26 13:31:25,689 execution finished:
> /home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/job_working_directory/000/31/galaxy_31.sh
> galaxy.jobs.output_checker INFO 2015-02-26 13:31:25,717 Job 31: Fatal error:
> Exit code 1 ()
> galaxy.jobs DEBUG 2015-02-26 13:31:25,784 setting dataset state to ERROR
>
> The error displayed in galaxy is just an empty VCF header (that why I asked
> about the error log)

Did you check the stdout and stderr via the web interface?

> Thank you for your help
>
> PS: By the way, my argument was -e 'variant!=null;' , why do I see '-e
> 'variant!=nullX'  in the log ?

You'll need to white list the semi-colon which Galaxy has replaced
as a security precaution (user free text can be exploited). See
<sanitizer> here:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter
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