Hi Pierre, The first example looks OK, very similar to this one of mine for example, so I am not sure what is breaking: https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada9... I would try adding more shell actions to debug this with echo statements? However, rather than using wget you could use the download_file action which can verify the checksum, and will also work on a Mac where wget is usually missing. Peter On Thu, Oct 20, 2016 at 8:03 AM, Pierre Lindenbaum <pierre.lindenbaum@univ-nantes.fr> wrote:

(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

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