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
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/
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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
___________________________________________________________ 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/
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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
___________________________________________________________ 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/
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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
___________________________________________________________ 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/
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
It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink
Am 03.01.2015 um 17:44 schrieb Waldron, Michael H: 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
___________________________________________________________ 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/
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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<mailto: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<mailto:bjoern.gruening@gmail.com>] Sent: Sunday, January 04, 2015 12:46 PM To: Waldron, Michael H; Björn Grüning; galaxy-dev@bx.psu.edu<mailto: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<mailto:bjoern.gruening@gmail.com>] Sent: Saturday, January 03, 2015 6:42 AM To: Waldron, Michael H; galaxy-dev@bx.psu.edu<mailto: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
___________________________________________________________ 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/
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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/
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
___________________________________________________________ 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/
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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/
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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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Hi Michael, I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help. If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases: https://wiki.galaxyproject.org/DevNewsBriefs We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand. Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems. --nate On Mon, Jan 5, 2015 at 10:34 AM, Waldron, Michael H <mwaldron@email.unc.edu> wrote:
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:
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'
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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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I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves. One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single platform. This frees you from having to support many different platforms and versions. Have you guys given this some thought? On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Michael,
I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help.
If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases:
https://wiki.galaxyproject.org/DevNewsBriefs
We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand.
Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems.
--nate
Hi Ryan, I have tried to collect a minimal set of dependencies you need to have installed: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList And we have a Galaxy Docker container that is working and should define and test a fresh Galaxy installation: https://github.com/bgruening/docker-galaxy-stable Please also have a look at the Galaxy playbook: https://github.com/galaxyproject/usegalaxy-playbook This defines a installation and deployment strategy of Galaxy for several platforms. I don't think that the Galaxy project is going to focus on one single platform. But this is only my opinion. I think one of Galaxy strength is, that it is working on everything besides Windows (without docker). Cheers, Bjoern Am 05.01.2015 um 23:36 schrieb Ryan G:
I hate to hijack this thread, but I was thinking about this over the holiday in how we are going to maintain a local up to date copy of Galaxy ourselves. One thought would be to standardize on a single supported platform aka an Amazon instance and make sure everything works on that single platform. This frees you from having to support many different platforms and versions. Have you guys given this some thought?
On Mon, Jan 5, 2015 at 12:05 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Michael,
I understand your frustration in this regard. We do make an effort to respond to and fix issues that people encounter when upgrading Galaxy releases. We've also made pretty significant strides in increasing the quality of our releases, including a feature freeze for at least 2 weeks prior to each release. The galaxy-dev mailing list is fairly active, as is our IRC channel (#galaxyproject on Freenode) for more real-time help.
If you're not familiar with the Galaxy News Briefs, these are the primary means of communicating the changes you should expect to see between Galaxy releases and any config changes that might be necessary between releases:
https://wiki.galaxyproject.org/DevNewsBriefs
We also recommend having a Test/QA Galaxy server (or cloning your production Galaxy instance) to test an upgrade before deploying it on your production instance(s) so most problems can be caught beforehand.
Unfortunately, due to the wide range of platforms, deployment scenarios, site-specific factors, and large scope of Galaxy functionality, we can't catch all potential issues. I don't think this is outside the rate typically experienced with major releases of large open source software, but it is still frustrating when it occurs. That said, we'll do our best to assist and improve documentation when you do encounter upgrade problems.
--nate
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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 [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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participants (6)
-
Björn Grüning -
John Chilton -
Martin Čech -
Nate Coraor -
Ryan G -
Waldron, Michael H