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

20 Oct 2016

      (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} > ${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

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

Pierre Lindenbaum