Hi all,

I am building a wrapper around BLAT, and have put it locally in a toolshed. However, the automatic installation of dependencies fails:

Tool dependency installation error:
[Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/database/tmp/tmp2J7K_L/blat

Note that there is a strange duplication in the path. Furthermore, on that Galaxy instance, the database is on /mnt/testgalaxydb/database instead of path mentioned in the error.

The tool_dependencies.xml matches the wrapper xml. blat is just downloaded from its url.

<?xml version="1.0"?>
    <package name="blat" version="1.0.0">
        <install version="1.0">
<action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
                <action type="move_file">
                <action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
The BLAT binary for linux x86_64 is retrieved from UCSC.

Thanks for helping me further.


Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team

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