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
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