galaxy-dev July 2013

galaxy-dev@lists.galaxyproject.org

133 participants
209 discussions

ToolShed dependencies KeyError: 'invalid_repository_dependencies'
by Peter Cock 08 Jul '13

08 Jul '13

Hi Greg, Previously my workflows had hard coded dependencies on the main Tool Shed, which currently is a bit of a problem on the Test Tool Shed. Therefore I'm update my Tool Shed workflows using a repository_dependencies.xml with implicit repository and revision fields (i.e. the latest revision within the current ToolShed). It worked for one example but not the other - this turned out to be my own error, but the Tool Shed did not handle it gracefully. Perhaps this class of error could be caught instead? Thanks! ---------------------------------------------------------------- This worked, secreted_protein_workflow, Revision: 2:aecb871dfe4c http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow Input: <?xml version="1.0"?> <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">  <repository name="tmhmm_and_signalp" owner="peterjc" />  <repository name="seq_filter_by_id" owner="peterjc" /> </repositories> ---------------------------------------------------------------- This failed, rxlr_venn_workflow, Revision: 3:65d174589251 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow On uploading the tar-ball I got this error in the browser: <quote> Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=20a9f7389ced5… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.upload:219 in upload >> invalid_repository_dependencies_message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict ) Module tool_shed.util.repository_dependency_util:252 in generate_message_for_invalid_repository_dependencies >> invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'invalid_repository_dependencies' ] KeyError: 'invalid_repository_dependencies' extra data full traceback text version This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. </quote> Input repository_dependencies.xml where for the tmhmm_and_signalp entry I am missing the 'n' in name: <?xml version="1.0"?> <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">  <repository ame="tmhmm_and_signalp" owner="peterjc" />  <repository name="seq_filter_by_id" owner="peterjc" />  <repository name="venn_list" owner="peterjc" /> </repositories> Output repository_dependencies.xml with mangled tmhmm_and_signalp entry: <?xml version="1.0"?> <repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool.">  <repository ame="tmhmm_and_signalp" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />  <repository changeset_revision="66d1ca92fb38" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />  <repository changeset_revision="51fe47a5a803" name="venn_list" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories> I corrected the ame/name error, and re-uploaded a fresh tar-ball which worked, Revision: 4:25e0ffd4f762 Peter

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Error Uploading Directory of Files
by Nicholas Kline 08 Jul '13

08 Jul '13

Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed this Galaxy documentation ( http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?act… ) to setup this feature: - Admin > Data Library > Add datasets > Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying "Job error (click name for more info)". Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 386, in __main__() File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File "/Users/administrator/galaxy-dist/tools/data_source/upload.py", line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq Questions: 1. Should we be concerned about this error? 2. If so, what is the right way to fix it? 3. If not, how do we remove the red error message next to each file: "Job error (click name for more info)" ? Thank you

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Galaxy on a server without internet connexion try to contact toolshed.g2.bx.psu.edu
by Ghislain Fournous 08 Jul '13

08 Jul '13

Hi, I installed Galaxy on a server located on a secure Network without internet connexion following this instructions: http://wiki.galaxyproject.org/Admin/Config/Eggs For an offline usage I changed the following parameters: Desable eggs check in run.sh FETCH_EGGS to 0 And the toolshed check option in universe_wsgi.ini enable_tool_shed_check = False On the first run Galaxy run, but when I tried to restart Galaxy try to contact toolshed.g2.bx.psu.edu : #--------------------------- The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz&o… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_p… raised the exception: <urlopen error [Errno -3] Temporary failure in name resolution> Traceback (most recent call last): File "/usr/local/Galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/usr/local/Galaxy/galaxy-dist/lib/galaxy/app.py", line 55, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/usr/local/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py", line 55, in verify_tools tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/usr/local/Galaxy/galaxy-dist/lib/tool_shed/util/common_util.py", line 67, in check_for_missing_tools return tool_shed_accessible, missing_tool_configs_dict UnboundLocalError: local variable 'missing_tool_configs_dict' referenced before assignment #--------------------------- I Fixed this problem by adding a enable_tool_shed_check check in lib/galaxy/app.py I'm new in the Galaxy World, so perhaps that is not an optimal way to fix this problem. diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -51,8 +51,9 @@ from galaxy.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. - from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) + if self.config.get_bool( 'enable_tool_shed_check', False ): + from tool_shed.galaxy_install.migrate.check import verify_tools + verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) # Object store manager self.object_store = build_object_store_from_config(self.config) # Setup the database engine and ORM Regards, Ghislain

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How were liftover and nib files generated?
by Perez, Ricardo 08 Jul '13

08 Jul '13

Dear all, When I rsync files from let say the following command: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/dm3 . The system will sync files that are related to genome aligments, liftover, and nibs. How did the Galaxy team generated this files? The reason I ask is because I would lather will like to generate similar files to custom genomes to be used in galaxy. Thank you for your time, --Ricardo Perez

2 1

[GSoC2013] Week 2 Accomplishments and Week 3 Plans
by Saket Choudhary 08 Jul '13

08 Jul '13

Not much accomplished this week. I plan to write one more blogspot detailing the datamodel I learnt about galaxy. http://galaxy-gsoc2013.blogspot.com/2013/07/week-2-accomplishments-and-week… On 24 June 2013 14:11, Saket Choudhary <saketkc(a)gmail.com> wrote: > Hi Everyone, > > > Just wrote a blog post for my Week1 tasks and Week 2 to-dos: > > http://galaxy-gsoc2013.blogspot.in/2013/06/week-1-accomplishments-and-week-… > > > I am maintaining a work log in this doc : > https://docs.google.com/document/d/1VCKCpKW6C_Tt1DYWi43GAN_Jo-nebkkj8Ctq7WL… > > > If you have any suggestions for the VCF4.1 issue or otherwise. please do let > me know. > > Thanks > > Saket Choudhary > Undergraduate > Dept. of Chemical Engineering > IIT Bombay >

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Regarding galaxy wrappers: "lumi", "DESeq" "edgeR"
by Sachit Adhikari 07 Jul '13

07 Jul '13

Hi, These are the R libraries. Have anyone written a wrapper for these libraries "lumi", "DESeq" "edgeR"? Thanks, Sachit

3 5

Postgresql database not working
by Sajoscha Sauer 07 Jul '13

07 Jul '13

Hi all, I just installed the newest version of Galaxy with: hg clone https://bitbucket.org/galaxy/galaxy-dist I use Apache httpd as proxy and ldap authentication. If I leave the database as it is set by default everything works fine. sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE But if I now change to postgres my histories cannot be fetched. I'm not sure how to explain it, but every time I refresh the history panel a new history is created. The database connection is fine, it also creates the history entries in the database, but something is wrong. Has someone an idea or can help? Thanks a lot! Cheers, Sajoscha

1 1

Question about bowtie2_indeces.loc
by Perez, Ricardo 07 Jul '13

07 Jul '13

Dear all, When adding a genome I understand that the format are added in the following way: <unique_build_id> <dbkey> <display_name> <file_base_path> My question is, what is the difference between the unique_build_id and the dbkey? Thank you for your time, --Ricardo Perez

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instance restart fails with AttributeError: 'module' object has no attribute 'DataManagerHistoryAssociation'
by Vipin TS 06 Jul '13

06 Jul '13

Hello dev-team, I am trying to upgrade our production instance to the latest release (to galaxy-dist) , somehow I am not able to restart the instance. Here is the log message I found: File "./scripts/paster.py", line 35, in <module> serve.run() File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "galaxy-prod-repo/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "galaxy-prod-repo/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "galaxy-prod-repo/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "galaxy-prod-repo/lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "galaxy-prod-repo/lib/galaxy/webapps/galaxy/buildapp.py", line 18, in <module> import galaxy.model.mapping File "galaxy-prod-repo/lib/galaxy/model/mapping.py", line 943, in <module> Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) AttributeError: 'module' object has no attribute 'DataManagerHistoryAssociation' Removing PID file paster.pid I am not clear about the error message here. any idea thank you, --/Vipin cBio MSKCC Ratsch Lab

2 1

phastCons scores all NaN
by diana 05 Jul '13

05 Jul '13

Hi all, I am a new user to Galaxy. Recently I uploaded a bed file to Galaxy and then converted it to hg18 format in order to run a phastCons scoring on it. The fields returned were all NaN, though. I then converted the hg18 format to hg17 in order to see if that would make a difference, but it still returned NaN each time. At this point, in order to test if it was simply my data that had a problem, I found and viewed a specific region in the UCSC genome browser to verify that it did, in fact, include regions with conservation, I entered that sequence into Galaxy in bed format and attempted to get phastCons scores for it, but still received NaN for the results. At this point, I have no idea what is going on. I believe that this must be a bug, since I am fairly certain that my bed files are in the correct format. All of these were run on the main Galaxy server on and off during the past week. If anyone could help me figure out what is wrong, I would appreciate it very much. Thanks, Diana

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galaxy-dev July 2013