Hi Joachim, your definition is working fine for me (latest galaxy-central 9895:e3455a092882). If have uploaded it to this test repository: http://testtoolshed.g2.bx.psu.edu/view/bgruening/precommit_test ... and was able to install it. blat has no executable flag, so I needed to add chmod +x into the definition. The next Galaxy stable will be out in one week, afaik. At that time it will work :) Cheers, Björn
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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