We reverted back to fastqc version 0.10.1 and that is working. Given that our current galaxy version is old and problematic to upgrade, going forward we're going to stand up a new separate galaxy installation on another server. We'll be able to test everything on it before switching over to it.
Thanks to all for the help. Mike ________________________________________ From: John Chilton [jmchil...@gmail.com] Sent: Monday, January 05, 2015 10:25 AM To: Waldron, Michael H Cc: Martin Čech; Björn Grüning; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy This looks like a bug - but unfortunately it appears you are running a fairly old version of Galaxy - I don't think the file lib/galaxy/util/shed_util.py has existed for the better part of a year. It should be possible to get the FastQC wrapper to work with the old version if you figure out the exact version of fastqc you need - but if you want to use the tool shed you will probably want to upgrade to the latest stable release of Galaxy. -John On Mon, Jan 5, 2015 at 9:17 AM, Waldron, Michael H <mwald...@email.unc.edu> wrote: > I attempted to install fastqc via the tool shed, and got an error. The log > information is listed below. The main error appears to be "too many values > to unpack". > > 152.2.204.5 - - [05/Jan/2015:09:09:00 -0400] "GET > /admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9 > HTTP/1.1" 500 - > "https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ca249a25748b71a3&changeset_revision=0b201de108b9"; > "Mozilla/5.0 (X11; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > Error - <type 'exceptions.ValueError'>: too many values to unpack > URL: > https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9 > File > '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', > line 143 in __call__ > app_iter = self.application(environ, start_response) > File > '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', > line 80 in __call__ > return self.application(environ, start_response) > File > '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', > line 91 in __call__ > return self.app( environ, start_response ) > File > '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', > line 132 in __call__ > return self.handle_request( environ, start_response ) > File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', > line 185 in handle_request > body = method( trans, **kwargs ) > File > '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', > line 216 in decorator > return func( self, trans, *args, **kwargs ) > File > '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', > line 1345 in prepare_for_install > shed_util.get_dependencies_for_repository( trans, tool_shed_url, > repo_info_dict, includes_tool_dependencies ) > File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py', > line 601 in get_dependencies_for_repository > installed_rd, missing_rd = > get_installed_and_missing_repository_dependencies_for_new_install( trans, > repo_info_tuple ) > File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/util/shed_util.py', > line 715 in > get_installed_and_missing_repository_dependencies_for_new_install > tool_shed, name, owner, changeset_revision = rd_tup > ValueError: too many values to unpack > > Configuration > ------------- > __file__: '/nas02/apps/galaxy-prod/galaxy-dist/universe_wsgi.ini' > admin_users: > 'roac...@email.unc.edu,kel...@email.unc.edu,mwald...@email.unc.edu,jen...@email.unc.edu' > allow_user_dataset_purge: 'True' > database_connection: 'postgres://galaxy@localhost/galaxy' > database_engine_option_server_side_cursors: 'True' > database_engine_option_strategy: 'threadlocal' > debug: 'False' > default_cluster_job_runner: 'drmaa://-q pgalaxy_q -M 41900000 /' > enable_quotas: 'True' > enable_tracks: 'True' > file_path: '/proj/galaxy' > ftp_upload_dir: 'database/ftp' > ftp_upload_site: 'galaxy.its.unc.edu:2021' > here: '/nas02/apps/galaxy-prod/galaxy-dist' > job_working_directory: '/proj/galaxy/job_working_directory' > len_file_path: 'tool-data/shared/ucsc/chrom' > library_import_dir: '/proj/seq/galaxy' > local_job_queue_workers: '10' > nglims_config_file: 'tool-data/nglims.yaml' > remote_user_maildomain: 'email.unc.edu' > retry_job_output_collection: '30' > start_job_runners: 'drmaa' > static_cache_time: '360' > static_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/' > static_enabled: 'True' > static_favicon_dir: > '/nas02/apps/galaxy-prod/galaxy-dist/static/favicon.ico' > static_images_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/images' > static_scripts_dir: '/nas02/apps/galaxy-prod/galaxy-dist/static/scripts/' > static_style_dir: > '/nas02/apps/galaxy-prod/galaxy-dist/static/june_2007_style/blue' > tool_config_file: 'tool_conf.xml,shed_tool_conf.xml' > tool_dependency_dir: '../tool_dependencies' > tool_path: 'tools' > use_interactive: 'False' > use_nglims: 'False' > use_remote_user: 'True' > > > WSGI Variables > -------------- > application: <paste.recursive.RecursiveMiddleware object at 0x1fa05fd0> > original_wsgi.url_scheme: 'http' > paste.cookies: (<SimpleCookie: VCLACTIVENODE='12' > VCLAUTH='laCke775oUL18xKNIRgrIGOkWV8TDHKwq647BxYTcK1NkdOlvh0%2B8glvFC%2BdvpkoiYg7qttH2AXyWKGmw2aqWVJKp%2BeLJFauRWutlotbDElWn6CfZYeYesGHlWgWMnWbxAW8EYmsmecDsM0xV3KW5%2BFrMdBpDdseXYKCEXzpIIvvwp7F8gX%2BU%2BEUjPE3lb4JzGWf3Ie9XgfEqlPycbiJXPHXCrsGkanB3NXDzJJeUwe9PFO5bc0%2BA1vP7X3YxYdfjLxVAK9ZVqv8tpVwkyh26Mc%2BJ6ei5j9oYmOgQSGdoBuI3y6JmQuivN0z0I6%2FdFy1LBAH74Ri%2FZMgdL7%2Bgjj79A%3D%3D' > VCLLOCALE='en_US' VCLSKIN='default' __unam='74abf65-13ed3051d32-51a5d500-40' > __utma='117910737.2001824546.1373325050.1407267272.1407768470.35' > __utmc='180505699' > __utmz='117910737.1401999139.26.11.utmcsr=help.unc.edu|utmccn=(referral)|utmcmd=referral|utmcct=/help/research-computing-application-matrix/' > _ga='GA1.2.83593674.1365452191' > _shibsession_64656661756c7468747470733a2f2f67616c6178792e6974732e756e632e6564752f73686962626f6c657468='_881cda95b24d6988ef78dd775a463719' > galaxysession='c6ca0ddb55be603a6569c0b408144f8320f2758b32c93176f6b2d0daddb6375a8a07f508556...f78dd775a463719') > paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] > paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at > 0x1f83e690> > paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at > 0x18ec9110> > paste.parsed_querystring: ([('tool_shed_url', > 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'), > ('changeset_revisions', '0b201de108b9')], > 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9') > 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 > webob._parsed_query_vars: (MultiDict([('tool_shed_url', > 'https://toolshed.g2.bx.psu.edu/'), ('repository_ids', 'ca249a25748b71a3'), > ('changeset_revisions', '0b201de108b9')]), > 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=ca249a25748b71a3&changeset_revisions=0b201de108b9') > wsgi process: 'Multithreaded' > ------------------------------------------------------------ > > > Mike Waldron > Systems Specialist > ITS - Research Computing Center > University of North Carolina at Chapel Hill > > ________________________________ > From: Martin Čech [mar...@bx.psu.edu] > Sent: Monday, January 05, 2015 8:06 AM > > To: Waldron, Michael H; Björn Grüning; galaxy-...@bx.psu.edu > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy > > Hi Mike, > > give it a shot for sure. If you want some details have a look at > https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial > > M. > > On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <mwald...@email.unc.edu> > wrote: >> >> It's mostly due to my lack of thorough knowledge about Galaxy. So should I >> just try to do the tool shed install by going to Admin->Tool Sheds and >> selecting fastqc from there? >> >> Mike Waldron >> Systems Specialist >> ITS - Research Computing Center >> University of North Carolina at Chapel Hill >> >> >> ________________________________________ >> From: Björn Grüning [bjoern.gruen...@gmail.com] >> Sent: Sunday, January 04, 2015 12:46 PM >> To: Waldron, Michael H; Björn Grüning; galaxy-...@bx.psu.edu >> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy >> >> Hi Mike, >> >> it can happen that wrappers versions do not work well with older/newer >> FASTQC versions. This is the reason we try to couple "binary" versions >> of tools to wrappers versions. >> >> Any reason you don't use the toolshed installation with dependencies? >> >> Cheers, >> Bjoern >> >> Am 03.01.2015 um 17:44 schrieb Waldron, Michael H: >> > It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink >> > points to it under tool-data/shared/jars: >> > >> > $ pwd >> > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars >> > >> > FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC >> > >> > >> > Mike Waldron >> > Systems Specialist >> > ITS - Research Computing Center >> > University of North Carolina at Chapel Hill >> > >> > >> > ________________________________________ >> > From: Björn Grüning [bjoern.gruen...@gmail.com] >> > Sent: Saturday, January 03, 2015 6:42 AM >> > To: Waldron, Michael H; galaxy-...@bx.psu.edu >> > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy >> > >> > Hi Michael, >> > >> > which version of the FASTQC wrapper are you running? Can you point us to >> > the exact build and toolshed version? >> > >> > Thanks, >> > Bjoern >> > >> > Am 02.01.2015 um 21:22 schrieb Waldron, Michael H: >> >> Having a problem with directing FastQC output in Galaxy. User is >> >> running a job whose command line looks like this: >> >> >> >> # FastQC cl = >> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc >> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files >> >> /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq >> >> >> >> Job output looks like this: >> >> >> >> ## odpath=None: No output found in None. Output for the run was: >> >> # FastQC cl = >> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc >> >> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files >> >> /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq >> >> Started analysis of SRR016862.fastq >> >> Approx 5% complete for SRR016862.fastq >> >> Approx 10% complete for SRR016862.fastq >> >> Approx 15% complete for SRR016862.fastq >> >> Approx 20% complete for SRR016862.fastq >> >> Approx 25% complete for SRR016862.fastq >> >> Approx 30% complete for SRR016862.fastq >> >> Approx 35% complete for SRR016862.fastq >> >> Approx 40% complete for SRR016862.fastq >> >> Approx 45% complete for SRR016862.fastq >> >> Approx 50% complete for SRR016862.fastq >> >> Approx 55% complete for SRR016862.fastq >> >> Approx 60% complete for SRR016862.fastq >> >> Approx 65% complete for SRR016862.fastq >> >> Approx 70% complete for SRR016862.fastq >> >> Approx 75% complete for SRR016862.fastq >> >> Approx 80% complete for SRR016862.fastq >> >> Approx 85% complete for SRR016862.fastq >> >> Approx 90% complete for SRR016862.fastq >> >> Approx 95% complete for SRR016862.fastq >> >> Analysis complete for SRR016862.fastq >> >> >> >> The job_working_directory/010/10467 directory is created, however it is >> >> empty. It appears this "odpath" needs to be set somehow? >> >> >> >> Does anyone know a solution for this? >> >> >> >> Mike Waldron >> >> Systems Specialist >> >> ITS - Research Computing Center >> >> University of North Carolina at Chapel Hill >> >> >> >> >> >> >> >> >> >> ___________________________________________________________ >> >> 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: >> >> https://lists.galaxyproject.org/ >> >> >> >> 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: >> https://lists.galaxyproject.org/ >> >> 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: > https://lists.galaxyproject.org/ > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
