Joachim,
I believe the behavior you're experiencing may be due to an issue that
was fixed between 9320:47ddf167c9f1 and the current stable branch. I
would recommend updating to the most recent stable branch of
galaxy-central.
--Dave B.
On 5/29/13 09:30:37.000, Joachim Jacob | VIB | wrote:
Strange. When I just wget that link in a terminal, do 'chmod +X blat'
and ./blat, it just works fine.
Could it be that the permissions need to be set by Galaxy?
Version info of the Tool Shed:
*****************************************
[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9320:47ddf167c9f1 tip
Use Galaxy's ErrorMiddleware since Paste's doesn't return
start_response. Fixes downloading tarballs from the Tool Shed when
use_debug = false.
branch: stable
commit: 5 modified, 271 unknown
update: (current)
[galaxy@galaxy galaxy-dist]$
*****************************************
Version info of the Galaxy integrating the tool shed repository:
*****************************************
parent: 9292:2cc8d10988e0 security_2013.04.08
Controllers/history: use get_history in switch_to_history
branch: stable
commit: 4 modified, 22 unknown (new branch head)
update: 11 new changesets (update)
*****************************************
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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___________________________________________________________
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