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 > >>>> > >>>> > >>>> ___________________________________________________________ > >>>> Please keep all replies on the list by using "reply all" > >>>> in your mail client. To manage your subscriptions to this > >>>> and other Galaxy lists, please use the interface at: > >>>> http://lists.bx.psu.edu/ > >>>> > >>>> To search Galaxy mailing lists use the unified search at: > >>>> http://galaxyproject.org/search/mailinglists/ > >> > >> ___________________________________________________________ > >> Please keep all replies on the list by using "reply all" > >> in your mail client. To manage your subscriptions to this > >> and other Galaxy lists, please use the interface at: > >> http://lists.bx.psu.edu/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
