Question: Tool.xml : correct way to define an environment_variable ?
0
gravatar for plindenbaum
2.1 years ago by
plindenbaum • 90
France
plindenbaum • 90 wrote:

I'm trying to create some tools.xml that use java. Those tools need to download some library (*.jar) files from http://central.maven.org/ and I want to create a variable $MYTOOLCLASSPATH containing the jars. I've tried the following xml :

    
    <tool_dependency>
      <package name="mytool" version="0.0.1">
        <install version="1.0">
          <actions>
            <action type="shell_command">wget -P "$REPOSITORY_INSTALL_DIR" "http://central.maven.org/lib1.jar"  "http://central.maven.org/lib2.jar"</action>
            <action type="set_environment">
                <environment_variable name="MYTOOLCLASSPATH" action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar</environment_variable>   
            </action>
          </actions>
        </install>
      </package>
    </tool_dependency>

the tool is defined in a macro.xml:

          (...)
          <token name="@MYJAVA@">
    java   -cp "\${MYTOOLCLASSPATH}" 
          </token>
          (...)

and called in my tool.xml:

        <command>@MYJAVA@ tool.Tool ${input} &gt; ${out} </command>

but It seems that $MYTOOLCLASSPATH is empty.

I've also tried to create a set_environment under tool_dependency:

<set_environment version="1.0">
   <environment_variable name="MYTOOLCLASSPATH" action="set_to">$REPOSITORY_INSTALL_DIR/lib1.jar:$REPOSITORY_INSTALL_DIR/lib2.jar</environment_variable>
</set_environment>

same problem: the $MYTOOLCLASSPATH remains empty

What's the correct way to define MYTOOLCLASSPATH ?

ADD COMMENT • link • modified 2.1 years ago by Bjoern Gruening ♦ 5.1k • written 2.1 years ago by plindenbaum • 90
1
gravatar for plindenbaum
2.1 years ago by
plindenbaum • 90
France
plindenbaum • 90 wrote:

the question was answered on http://dev.list.galaxyproject.org/Tool-xml-correct-way-to-define-an-environment-variable-td4670165.html

ADD COMMENT • link written 2.1 years ago by plindenbaum • 90
1
gravatar for Bjoern Gruening
2.1 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Pierre,

how much chocolate do I need to send you that you try bioconda and use this as dependency resolver for your tool?

For example see this one here: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/meta.yaml

Cheers, Bjoern

ADD COMMENT • link written 2.1 years ago by Bjoern Gruening ♦ 5.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour