The problem is most likely in ~/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py, line 100. 1. current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) 2. while dir is set a couple of lines before as: dir = workdir (line 78). workdir is the temporary directory. 3. current_dir is then used by common_util.move_file on line 111. This explains the duplication in the path that I observed. It does not yet explain why the temporary directory is created in the wrong location. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 05/29/2013 03:08 PM, Greg Von Kuster wrote:
Hello Joachim,
This URL does not properly download blat. The Firefox browser determines it as a text file, while Safari displays it. This is the cause of the problem. Is there a different URL to download blat that actually downloads it as an archive os some kind?
Greg Von Kuster
On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote:
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"?> <tool_dependency> <package name="blat" version="1.0.0"> <install version="1.0"> <actions> <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action> <action type="move_file"> <source>blat</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> The BLAT binary for linux x86_64 is retrieved from UCSC. </readme> </package> </tool_dependency> *************************
Thanks for helping me further.
Cheers, Joachim
-- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team
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