Ok, we have run several previous version of fastqc with it, we'll try one of those. Our history of galaxy upgrade attempts has been very problematic. Things always seem to break, items disappear from menus, and I'm lost in trying to figure out the problems, so we tend to leave it alone. Mike ________________________________________ From: John Chilton [jmchilton@gmail.com] Sent: Monday, January 05, 2015 10:25 AM To: Waldron, Michael H Cc: Martin Čech; Björn Grüning; galaxy-dev@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 <mwaldron@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: 'roachjm@email.unc.edu,kelkar@email.unc.edu,mwaldron@email.unc.edu,jennyw@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 [marten@bx.psu.edu] Sent: Monday, January 05, 2015 8:06 AM
To: Waldron, Michael H; Björn Grüning; galaxy-dev@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 <mwaldron@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.gruening@gmail.com] Sent: Sunday, January 04, 2015 12:46 PM To: Waldron, Michael H; Björn Grüning; galaxy-dev@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.gruening@gmail.com] Sent: Saturday, January 03, 2015 6:42 AM To: Waldron, Michael H; galaxy-dev@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
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