Re: [galaxy-dev] custom java tools.xml : problem with classpath

26 Feb 2015


      On Thu, Feb 26, 2015 at 12:38 PM, Pierre Lindenbaum
<pierre.lindenbaum@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

Re: [galaxy-dev] custom java tools.xml : problem with classpath

Peter Cock