- galaxy-dev - lists.galaxyproject.org

Join the HOMER Galaxy wrapper development!
by Bjoern Gruening 13 Aug '13

13 Aug '13

Hi Galaxy Tool developers! I have started to integrate the HOMER suite into Galaxy. My initial attempt can be found here: https://github.com/bgruening/galaxytools/tree/master/homer Currently, we make use of: - Tool Shed definitions of all required 3rd Party Software - datatype definitions - loc files to define different HOMER datasets - macros - compostite datatypes (html output) I think that project can be a good start to learn Galaxy Tool development with all its simple and enhanced features. Also HOMER is a complex suite and you can add small and really big features if you like. If you are interested but did not have any experience in Tool development, do not hesitate to ask. I will try to help and explain as much as I can. For the beginning I included only 3 tools, and only one of them with a bunch of parameters. So there are many things to do ... If anyone is interested in leaning Galaxy Tool development and want to contribute. Fell free to join and contact me. Cheers, Bjoern P.S. I do not mind to merge my changes to the already existing repository from Kevin, but I was not able to contact him. http://toolshed.g2.bx.psu.edu/view/kevyin/homer

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Running Jobs:
by Jurgens de Bruin 13 Aug '13

13 Aug '13

Hey All, Apologies for all the questions on the mailing list...I am having a lot of difficulty getting our local Galaxy working. Currently I have galaxy running but when I try run a job it just stays on "Job is waiting to run" and never runs. I have read the guide and wiki but can't seem to solve my problem at all... The output of sh run.sh: sh run.sh /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/boto-2.5.2-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Whoosh-0.3.18-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/amqplib-0.6.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pexpect-2.4-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Babel-0.9.4-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Mako-0.4.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebHelpers-0.2-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebOb-0.8.5-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Routes-1.12.3-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/wchartype-0.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/elementtree-1.2.6_20050316-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/docutils-0.7-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/PasteDeploy-1.5.0-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Paste-1.7.5.1-py2.6.egg, /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/lib, /scratch/sysusers/galaxy/galaxy_env/lib64/python26.zip, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/plat-linux2, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-tk, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-old, /scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-dynload, /usr/lib64/python2.6, /usr/lib/python2.6, /scratch/sysusers/galaxy/galaxy_env/lib/python2.6/site-packages /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname> Starting server in PID 59419. serving on 0.0.0.0:8989 view at http://127.0.0.1:8989 /scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927: SAWarning: The IN-predicate on "request_type.id" was invoked with an empty sequence. This results in a contradiction, which nonetheless can be expensive to evaluate. Consider alternative strategies for improved performance. 155.240.187.100 - - [13/Aug/2013:12:28:36 +0000] "GET /root HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /root/welcome HTTP/1.1" 302 - "http://155.240.187.2:8989/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /history HTTP/1.1" 200 - "http://155.240.187.2:8989/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /history/get_display_application_links HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:30 +0000] "POST /tool_runner HTTP/1.1" 200 - "http://genome.ucsc.edu/cgi-bin/hgTables" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:30 +0000] "GET /history HTTP/1.1" 200 - "http://155.240.187.2:8989/tool_runner" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:31 +0000] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:31 +0000] "GET /history/get_display_application_links HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" 155.240.187.100 - - [13/Aug/2013:12:32:35 +0000] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - " http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0" I would I check to see if a job is passed on to torque via drmaa? Any help would be appreciated -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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Galaxy behind a authenticated proxy Server
by Jurgens de Bruin 13 Aug '13

13 Aug '13

To All, I am in the process of setting-up a local galaxy server. To access the internet we are required to go trough a authenticated proxy server before any web-services can be accessed. So my questions is how will galaxy handle this? -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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scripting galaxy installs / toolshed
by Ido Tamir 13 Aug '13

13 Aug '13

Hi, we would like to coordinate with another institution and their galaxy setup regarding tools installed from multiple toolsheds (and their position/group in the panel) should be similar. Is there a way to achieve that with scripting? Suppose I would start the galaxy install from scratch also at our site. Could we somehow coordinate our installation? thank you very much, ido

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Error when running test
by Jurgens de Bruin 13 Aug '13

13 Aug '13

Hi All, I am getting the following error in run_functional_tests.html when running sh run_functional_tests.sh. Any idea what is happening? Thanks Traceback (most recent call last): File "/usr/lib64/python2.6/unittest.py", line 269, in run self.setUp() File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/test/base/twilltestcase.py", line 53, in setUp self.home() File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/test/base/twilltestcase.py", line 1141, in home self.visit_url( self.url ) File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/test/base/twilltestcase.py", line 1324, in visit_url tc.code( 200 ) File "/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/twill-0.9-py2.6.egg/twill/commands.py", line 133, in code should_be)) TwillAssertionError: code is 401 != 200 -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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Galaxy Distribution Aug 12, 2013
by Jennifer Jackson 13 Aug '13

13 Aug '13

*Galaxy Distribution **Aug 12, 2013* / / /////http://bit.ly/galaxy20130812/ *Highlights:* * Upgrades to *Data Manager* including improved installation actions * *Visualization* Framework tunings, plus updates to *Phyloviz*, *Scatterplot*, and *Trackster *** * *Workflows* include new reproducibility controls and editing features * Multiple *Tool Shed* enhancements, features, and tunings * Plus additional updates to the *UI*, *Admin* and *Core*, and *API*, an important *Security Fix* reminder, and *Bug Fixes* http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2013.08.12 /Thanks for using Galaxy,/ The Galaxy Team -- Jennifer Hillman-Jackson http://galaxyproject.org

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Public production instance page is not loading properly with latest stable release
by Vipin TS 12 Aug '13

12 Aug '13

Hi Dev-team, I have updated my production instance to 10201:ebe87051fadf, The page is not loading properly. Please find the log message as following. serving on 0.0.0.0:8081 view at http://127.0.0.1:8080 X.X.X.X - - [12/Aug/2013:16:58:35 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" X.X.X.X - - [12/Aug/2013:16:58:36 -0400] "GET /root/welcome HTTP/1.1" 302 - "https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" X.X.X.X - - [12/Aug/2013:16:58:36 -0400] "GET /history HTTP/1.1" 200 - " https://galaxy.cbio.mskcc.org/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0" 66.249.72.219 - - [12/Aug/2013:17:00:02 -0400] "GET /history/delete_current?purge=True HTTP/1.1" 500 - "-" "Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'users_shared_with' URL: https://galaxy.cbio.mskcc.org/history/delete_current?purge=True File '/codebase/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/codebase/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/codebase/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/codebase/lib/galaxy/webapps/galaxy/controllers/history.py', line 540 in delete_current if history.users_shared_with: AttributeError: 'NoneType' object has no attribute 'users_shared_with' CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: '*/*' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_CONNECTION: 'Keep-Alive' HTTP_FROM: 'googlebot(at)googlebot.com' HTTP_HOST: 'galaxy.cbio.mskcc.org' HTTP_USER_AGENT: 'Mozilla/5.0 (compatible; Googlebot/2.1; + http://www.google.com/bot.html)' HTTP_X_FORWARDED_FOR: '66.249.72.219' HTTP_X_FORWARDED_HOST: 'galaxy.cbio.mskcc.org' HTTP_X_FORWARDED_SERVER: 'galaxy.cbio.mskcc.org' HTTP_X_URL_SCHEME: 'https' ORGINAL_HTTP_HOST: 'localhost:8081' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history/delete_current' QUERY_STRING: 'purge=True' REMOTE_ADDR: '66.249.72.219' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x8c38850> is_api_request: False original_wsgi.url_scheme: 'http' paste.cookies: (<SimpleCookie: >, '') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x96d1dd0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x99e9f10> paste.parsed_querystring: ([('purge', 'True')], 'purge=True') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: '28651434039211e389a390b11c087d99' webob._parsed_query_vars: (MultiDict([('purge', 'True')]), 'purge=True') wsgi process: 'Multithreaded' ------------------------------------------------------------ X.X.X.X - - [12/Aug/2013:17:00:42 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.34 (KHTML, like Gecko) rekonq Safari/534.34" Is that something missing here, Thanks V ipin

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How can I shorten refresh time?
by Ramon Tiburski 12 Aug '13

12 Aug '13

When I run some tool or some workflow, delay about 2 or 3 seconds to refresh the page, where can I change it? Thank you...

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[GSoC2013] Week 7 and Week 8 Update
by Saket Choudhary 12 Aug '13

12 Aug '13

Hi Everyone, Here is an update for the last 2 weeks: http://galaxy-gsoc2013.blogspot.com/2013/08/week-7-and-week-8-update.html Saket

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Adding GATK tools to Galaxy Cloudman
by Iry Witham 12 Aug '13

12 Aug '13

Hi Team, I am trying to get GATK tools added to my cloud instance and keep getting the following error: [Errno 2] No such file or directory: '/mnt/galaxyData/tmp/tmpszWRLP/GenomeAnalysisTKLite-2.3-9-gdcdccbb/GenomeAnalysisTK.jar'. Then when I try to install it again I get the following: All selected tool dependencies are already installed. I also get the following error: Initializing repository installation failed. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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