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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