Joachim, I'm unable to duplicate that error, what revision of Galaxy and the tool shed code are you running? The path mentioned in the error message is a temporary working directory that is created for downloading and processing files needed for a tool dependency. Had the installation succeeded, the required files would have been moved to a path under /mnt/testgalaxydb/database, as expected. --Dave B. On 5/29/13 06:54:39.000, 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