Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not solve the problem.

In Trello, this card #584 was posted, mentioning installing compiled binaries is not yet possible, apparently. This is what I experience I believe. (BTW, the search bar at the top of Trello does not work for me - Galaxy board is only pinned to my account, so I cannot apparently search that way)

Thanks,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 05/29/2013 07:43 PM, Dave Bouvier wrote:
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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