Re: [galaxy-dev] Create a package with binaries

Hi AK,

Am 22.12.2014 um 10:56 schrieb KRESS Arnaud (ESP):

Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message:

mytool.sh: line 14: mytool: unknown command

It seems that the PATH was not correctly set. What am I doing wrong ?

My directory tree in my package: . ├── mytool.sh ├── mytool.xml ├── bin │ └── mytool └── tool_dependencies.xml

Here is my tool_dependencies.xml file content:

<?xml version="1.0"?>

<tool_dependency> <package name="mytool" version="1.0"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action>

INSTALL_DIR is not the directory where your XML file is located. The correct way would be if you download/compile your binary and move it to INSTALL_DIR.

An alternative would be to put $REPOSITORY_INSTALL_DIR/bin in your path.

Ciao, Bjoern

        </actions>
    </install>
    <readme>
    </readme>
</package>

</tool_dependency>

Thank you, AK ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

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