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: '[email protected],[email protected],[email protected],[email protected]' 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 [[email protected]] Sent: Monday, January 05, 2015 8:06 AM To: Waldron, Michael H; Björn Grüning; [email protected] 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 <[email protected]<mailto:[email protected]>> 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 [[email protected]<mailto:[email protected]>] Sent: Sunday, January 04, 2015 12:46 PM To: Waldron, Michael H; Björn Grüning; [email protected]<mailto:[email protected]> 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 > [[email protected]<mailto:[email protected]>] > Sent: Saturday, January 03, 2015 6:42 AM > To: Waldron, Michael H; [email protected]<mailto:[email protected]> > 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/
