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