[galaxy-dev] Tool.xml : correct way to define an environment_variable ?

[Pierre Lindenbaum]

(cross-posted at https://biostar.usegalaxy.org/p/20220/ )

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 :

        <?xml version="1.0" encoding="UTF-8"?>
        <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 base java command is defined as a token in 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

Where Am i wrong ? What's the correct way to define MYTOOLCLASSPATH ?



Thanks,

Pierre


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