August 2014 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Main Galaxy Tool Shed is running the next-stable branch
by Eric Kuyt 06 Aug '14

06 Aug '14

Hi Greg, Could there be some problems with https://toolshed.g2.bx.psu.edu/ I have some troubles installing toolshed tools in our galaxy. When I try installing for instance 'suite_samtools_0_1_19', I am presented with a 500 error. I tried then pulling a new stable galaxy from bitbucket, which seems to have the same problem. Maybe I'm doing something wrong both times or toolshed is having problems. I opt for the latter of course. -- part of galaxy traceback -- File '/usr/lib/python2.7/urllib2.py', line 527 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error Thanks, Eric On 29 July 2014 23:35, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello all, > > The main Galaxy Tool Shed is now running the next-stable branch ( > e6813f244a2a (next-stable) tip ) in preparation for next upcoming Galaxy > release. Please let us know if you encounter anything strange or broken > and we'll get things fixed asap. The main Tool Shed will be updated to the > stable branch when it is created for the upcoming Galaxy release. > > Thanks very much, > > Greg Von Kuster > > > > ___________________________________________________________ > 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/ >

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error using get( $__user_id__ ) in xml file in new Galaxy
by Neil.Burdett＠csiro.au 06 Aug '14

06 Aug '14

Hi, I have recently upgraded Galaxy from a version I had last year. In my tool xml file I could state: ${ __app__.model.User.get( $__user_id__ ).api_keys[0].key } in the <command> section to get the user's API. However, after updating to the current version of Galaxy I get the following error when using this entry in the xml file: Traceback (most recent call last): File "/home/bmladmin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job job_wrapper.prepare() File "/home/bmladmin/galaxy-dist/lib/galaxy/jobs/__init__.py", line 712, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py", line 348, in build self.__build_command_line( ) File "/home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py", line 364, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/home/bmladmin/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/bmladmin/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1407207170_7_53169.py", line 92, in respond NotFound: cannot find 'get' while searching for 'get' Any ideas? Thanks Neil

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Serious start-up delay in next-stable
by Björn Grüning 06 Aug '14

06 Aug '14

Hi all, does anyone encountered a long start-up delay with the recent next-stable and starting a instance from scratch? For me its hanging at: tool_shed.galaxy_install.migrate.check DEBUG 2014-08-05 18:39:45,207 psycopg2 egg successfully loaded for postgres dialect for 3-5 minutes. Cheers, Bjoern

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samtools installation error
by Beginner TI 05 Aug '14

05 Aug '14

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Re: [galaxy-dev] Galaxy Security Vulnerability
by Dooley, Damion 05 Aug '14

05 Aug '14

Does this apply to all past galaxy installs? I have an older galaxy site I've been wanting to phase out rather than upgrade. For now I'd like to use a patch but site version (parent: 7148:17d57db9a7c0 ) predates any of the tags. I presume I'd have to just implement the patch by hand? Regards, Damion Message: 7 Date: Thu, 31 Jul 2014 14:55:57 -0400 From: Nate Coraor <nate(a)bx.psu.edu> To: Galaxy Development <galaxy-dev(a)lists.bx.psu.edu>, galaxy-announce(a)lists.bx.psu.edu Subject: [galaxy-dev] Galaxy Security Vulnerability Message-ID: <D482333D-384E-49C8-8DD8-C752E4B0AF76(a)bx.psu.edu> Content-Type: text/plain; charset="us-ascii" A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python "pickle" functionality to decode state information from tool forms. Because pickles can be used to instantiate arbitrary Python objects, tool states could be constructed to exploit this vulnerability. ... - pickle-2013.01.13.patch - This patch should apply cleanly (with offset/fuzz) to releases from 2013.01.13 up to 2013.08.12, and possibly older versions of Galaxy as well. Available at: https://depot.galaxyproject.org/patch/pickle-2013.01.13.patch

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job not starting on cluster
by Langhorst, Brad 05 Aug '14

05 Aug '14

I’m not aware of any recent changes to the configuration of galaxy… It seems that jobs are not being distributed at the moment. I have 2 job handlers... It seems that when I restart them only a single job is queued, it has an error and then sticks on "Cleaning up external metadata files” forever. any ideas? I have 700+ jobs in the queue and would like to get them running asap... one hanlder just stays at Starting server in PID 4868. serving on http://127.0.0.1:8090 here’s the log from the other. Starting server in PID 4873. serving on http://127.0.0.1:8091 galaxy.jobs DEBUG 2014-08-05 17:34:08,388 (125206) Working directory for job is: /mnt/galaxy/data/galaxy/job_working_directory/000/125/125206 galaxy.jobs.handler DEBUG 2014-08-05 17:34:08,410 (125206) Dispatching to gridengine runner galaxy.jobs DEBUG 2014-08-05 17:34:08,479 (125206) Persisting job destination (destination id: gridengine) galaxy.jobs.handler INFO 2014-08-05 17:34:08,498 (125206) Job dispatched galaxy.tools.deps DEBUG 2014-08-05 17:34:08,862 Building dependency shell command for dependency 'bedtools2' galaxy.tools.deps WARNING 2014-08-05 17:34:08,865 Failed to resolve dependency on 'bedtools2', ignoring galaxy.jobs.runners DEBUG 2014-08-05 17:34:08,966 (125206) command is: bedtools --version > /mnt/galaxy/data/galaxy/tmp/GALAXY_VERSION_STRING_125206 2>&1; bedtools intersect -v -a /mnt/galaxy/data/galaxy/user-data/000/170/dataset_170995.dat -b /mnt/galaxy/data/galaxy/user-data/000/169/dataset_169046.dat > "/mnt/galaxy/data/galaxy/user-data/000/170/dataset_170999.dat"; return_code=$?; cd /mnt/galaxy/data/galaxy/galaxy-dist; /mnt/galaxy/data/galaxy/galaxy-dist/set_metadata.sh /mnt/galaxy/data/galaxy/user-data /mnt/galaxy/data/galaxy/job_working_directory/000/125/125206 . /mnt/galaxy/data/galaxy/galaxy-dist/universe_wsgi.ini /mnt/galaxy/data/galaxy/tmp/tmpLCBPvF /mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/galaxy.json /mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/metadata_in_HistoryDatasetAssociation_194826_qIy33T,/mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/metadata_kwds_HistoryDatasetAssociation_194826_SJhToq,/mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/metadata_out_HistoryDatasetAssociation_194826_4Lf956,/mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/metadata_results_HistoryDatasetAssociation_194826_YzEZK8,,/mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/metadata_override_HistoryDatasetAssociation_194826_19nZAm; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2014-08-05 17:34:08,994 (125206) submitting file /mnt/galaxy/data/galaxy/job_working_directory/000/125/125206/galaxy_125206.sh galaxy.jobs.runners.drmaa INFO 2014-08-05 17:34:09,023 (125206) queued as 1539118 galaxy.jobs DEBUG 2014-08-05 17:34:09,048 (125206) Persisting job destination (destination id: gridengine) galaxy.jobs.runners.drmaa DEBUG 2014-08-05 17:34:09,451 (125206/1539118) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2014-08-05 17:34:11,510 (125206/1539118) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2014-08-05 17:34:31,208 (125206/1539118) state change: job finished normally galaxy.jobs DEBUG 2014-08-05 17:34:31,440 setting dataset state to ERROR galaxy.jobs INFO 2014-08-05 17:34:31,652 Collecting job metrics for <galaxy.model.Job object at 0x7f42e030f850> galaxy.jobs DEBUG 2014-08-05 17:34:31,664 job 125206 ended galaxy.datatypes.metadata DEBUG 2014-08-05 17:34:31,665 Cleaning up external metadata files -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist

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PHYLIP
by Philippe Moncuquet 05 Aug '14

05 Aug '14

Hi, I haven't been able to find any implementation of the PHYLIP tools into Galaxy. I know some datatype are part of the emboss datatypes but what about the tools ? I reckon I am not the only one looking for this so I fear I might have missed something, if this is the case could you please point in the right direction to look ? Regards, Philip

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cufflinks suite 2.2.1
by Geert Vandeweyer 04 Aug '14

04 Aug '14

Hi all, I've updated the tool wrappers for the cufflinks tools to options supported by cufflinks 2.2.1. I've also added the cuffquant and cuffnorm tools, together with the cxb datatype. As discussed with Jeremy, these updates were welcome :-) Everything is available on the test toolshed, tested and installed on at least one instance (http://biomina.be/app/galaxy) although mixing main and test toolshed installations doesn't work well. The tools are present twice. Therefore, feel free to integrate the updated wrappers & tools into the main cufflinks package (by devteam) after further testing. Best, geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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start and end times?
by Evan Bollig 04 Aug '14

04 Aug '14

Jobs executed in the workflow appear to have a creation time, but no execution start and end time listed. How does one determine when something executed? I'd like to know exactly where the time is spent computing... -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Re: [galaxy-dev] "HTTPerror : HTTP error 307 : temporary redirect"
by Perley, Danielle 04 Aug '14

04 Aug '14

Solved! After finding documentation indicating that changing the URL of the test toolshed from http to https in the tool_sheds_config.xml file solved some redirection issues, I tried the same thing for the URL of the main toolshed. Message: 7 Date: Fri, 1 Aug 2014 20:30:14 +0000 From: "Perley, Danielle" <danielle.perley(a)med.und.edu> To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: [galaxy-dev] Error while installing tools from main toolshed: "HTTPerror : HTTP error 307 : temporary redirect" Message-ID: <1406925112700.23132(a)med.und.edu> Content-Type: text/plain; charset="iso-8859-1" Hi, I'm trying to install tools from the main toolshed, but I keep getting the same error regardless of the tool that I'm installing HTTPError: HTTP Error 307: Temporary Redirect URL: http://localhost:8080/admin_toolshed/prepare_for_install?tool_shed_url=http… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:377 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1116 in prepare_for_install view >> updating=updating ) Module tool_shed.util.common_install_util:110 in get_dependencies_for_repository view >> all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:451 in get_required_repo_info_dicts view >> response = urllib2.urlopen( request ).read() Module urllib2:127 in urlopen view >> return _opener.open(url, data, timeout) Module urllib2:410 in open view >> response = meth(req, response) Module urllib2:523 in http_response view >> 'http', request, response, code, msg, hdrs) Module urllib2:442 in error view >> result = self._call_chain(*args) Module urllib2:382 in _call_chain view >> result = func(*args) Module urllib2:608 in http_error_302 view >> new = self.redirect_request(req, fp, code, msg, headers, newurl) Module urllib2:569 in redirect_request view >> raise HTTPError(req.get_full_url(), code, msg, headers, fp) HTTPError: HTTP Error 307: Temporary Redirect I've just installed Galaxy locally for the first time on a Mac OS 10.9.3. The only changes I've made to the universe_wsg.ini file are: setting host=0.0.0.0 (The error also occurred with host=127.0.0.1?) specifying a full path for Tool_depenendency_dir giving myself administrator privileges with admin_users=myemail any ideas? Danielle

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