Hi Anne,

as far as I know Galaxy does not have an API endpoint to uninstall
repositories. I would use an admin interface for this - the process of
uninstalling is pretty fast and unless you have some crazy number of
installed tools it should be done quick.

M.

On Thu Feb 05 2015 at 12:24:03 PM Anne Pajon <anne.pa...@cruk.cam.ac.uk>
wrote:

> Hi Martin,
>
> Many thanks for your answer, and sorry for this late reply I've been off
> sick.
>
> In order to ease my migration, I am looking into reducing the number of
> tools installed that are not in used. We do run a cut down version of
> galaxy with much fewer tools that currently in Galaxy Main, but the tool
> migration scripts have installed lots of tools within my system that are
> not needed as I see them in 'Installed tool shed repositories' . I wish I
> could find a way to automatically remove installed tools that are not in
> use. Any ideas if such a script already exists? Or should I write it
> myself? Any guidance on where to start would be great. Many thanks in
> advance for your help.
>
> Cheers,
> Anne.
>
> On 30 Jan 2015, at 15:46, Martin Čech <mar...@bx.psu.edu> wrote:
>
> > Hi Anne,
> >
> > moving the whole Galaxy installation is a tough job and we do not really
> have a good process for it. Your problem is most probably caused by the
> inconsistency in the DB. The path to the shed_tool_conf.xml is stored there
> and the changes you made to the location of the installation did not
> propagate there.
> >
> > Please have a look at the following script that Dave B. made:
> https://gist.github.com/InitHello/d208cd056baf088aca1f
> >
> > This script will soon be part of the distribution (in /scripts) and
> should help you solving your issues.
> >
> > Thank you for using Galaxy.
> >
> > Martin, Galaxy Team
> >
> > On Thu Jan 29 2015 at 11:47:19 AM Anne Pajon <anne.pa...@cruk.cam.ac.uk>
> wrote:
> > Hi there,
> >
> > I am currently trying to migrate our Galaxy production server onto new
> hardware and I am facing many challenges. Recently I've been unable to
> update tools from the tool shed. During the migration I've moved across the
> files, the data, the tools and their dependencies as well as the database.
> But I am getting this error while trying to update any tools that are
> marked 'Updates are available in the Tool Shed for this revision' from the
> GUI: Admin > Manage installed tool shed repositories > fasta_formatter menu
> Get updates:
> >
> > Internal Server Error
> >
> > Galaxy was unable to successfully complete your request
> >
> > An error occurred.
> >
> > This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
> > The error has been logged to our team.
> >
> > Here is the log from paster.log:
> >
> > 10.20.13.16 - - [29/Jan/2015:16:43:45 +0100] "GET
> /admin_toolshed/update_to_changeset_revision?tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=fasta_formatter&;
> owner=devteam&changeset_revision=8f0ae92440b8&latest_changeset_revision=
> 1dbb5181c327&latest_ctx_rev=1 HTTP/1.1" 500 - "http://bioinf-gal001:8080/
> admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_
> checkboxes=false&advanced_search=false&f-deleted=False&
> f-free-text-search=fasta_formatter" "Mozilla/5.0 (Macintosh; Intel Mac OS
> X 10.8; rv:35.0) Gecko/20100101 Firefox/35.0"
> > Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no
> attribute 'get'
> > URL: http://bioinf-gal001:8080/admin_toolshed/update_to_
> changeset_revision?tool_shed_url=https://toolshed.g2.bx.
> psu.edu/&name=fasta_formatter&owner=devteam&changeset_
> revision=8f0ae92440b8&latest_changeset_revision=
> 1dbb5181c327&latest_ctx_rev=1
> > File 
> > '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
> >   app_iter = self.application(environ, sr_checker)
> > File 
> > '/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> line 84 in __call__
> >   return self.application(environ, start_response)
> > File 
> > '/mnt/nfs/data/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> line 633 in __call__
> >   return self.application(environ, start_response)
> > File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 132 in __call__
> >   return self.handle_request( environ, start_response )
> > File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 190 in handle_request
> >   body = method( trans, **kwargs )
> > File 
> > '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py',
> line 87 in decorator
> >   return func( self, trans, *args, **kwargs )
> > File '/mnt/nfs/data/galaxy/galaxy-dist/lib/galaxy/webapps/
> galaxy/controllers/admin_toolshed.py', line 1953 in
> update_to_changeset_revision
> >   persist=True )
> > File '/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/galaxy_
> install/metadata/installed_repository_metadata_manager.py', line 31 in
> __init__
> >   metadata_dict=metadata_dict, user=None )
> > File 
> > '/mnt/nfs/data/galaxy/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py',
> line 60 in __init__
> >   self.metadata_dict = { 'shed_config_filename' :
> self.shed_config_dict.get( 'config_filename', None ) }
> > AttributeError: 'NoneType' object has no attribute 'get'
> >
> >
> > CGI Variables
> > -------------
> >   CONTENT_LENGTH: '0'
> >   HTTP_ACCEPT: 'text/html,application/xhtml+
> xml,application/xml;q=0.9,*/*;q=0.8'
> >   HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> >   HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
> >   HTTP_CONNECTION: 'keep-alive'
> >   HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a44ec9cad39b012
> 02307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9'
> >   HTTP_HOST: 'bioinf-gal001:8080'
> >   HTTP_REFERER: 'http://bioinf-gal001:8080/admin_toolshed/browse_
> repositories?async=false&sort=name&page=1&show_item_
> checkboxes=false&advanced_search=false&f-deleted=False&
> f-free-text-search=fasta_formatter'
> >   HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8;
> rv:35.0) Gecko/20100101 Firefox/35.0'
> >   PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
> >   QUERY_STRING: 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=
> fasta_formatter&owner=devteam&changeset_revision=
> 8f0ae92440b8&latest_changeset_revision=1dbb5181c327&latest_ctx_rev=1'
> >   REMOTE_ADDR: '10.20.13.16'
> >   REQUEST_METHOD: 'GET'
> >   SERVER_NAME: '0.0.0.0'
> >   SERVER_PORT: '8080'
> >   SERVER_PROTOCOL: 'HTTP/1.1'
> >
> >
> > WSGI Variables
> > --------------
> >   application: <paste.recursive.RecursiveMiddleware object at
> 0x7f34f7a50590>
> >   is_api_request: False
> >   paste.cookies: (<SimpleCookie: galaxysession='
> c6ca0ddb55be603a44ec9cad39b01202307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9'>,
> 'galaxysession=c6ca0ddb55be603a44ec9cad39b012
> 02307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9')
> >   paste.expected_exceptions: [<class 'paste.httpexceptions.
> HTTPException'>]
> >   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> object at 0x7f34f7a50550>
> >   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0x7f34f76ef1d0>
> >   paste.parsed_querystring: ([('tool_shed_url', '
> https://toolshed.g2.bx.psu.edu/'), ('name', 'fasta_formatter'), ('owner',
> 'devteam'), ('changeset_revision', '8f0ae92440b8'),
> ('latest_changeset_revision', '1dbb5181c327'), ('latest_ctx_rev', '1')],
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=
> fasta_formatter&owner=devteam&changeset_revision=
> 8f0ae92440b8&latest_changeset_revision=1dbb5181c327&latest_ctx_rev=1')
> >   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
> >   request_id: 'fdaf9004a7d511e49d63005056a77528'
> >   webob._parsed_query_vars: (MultiDict([('tool_shed_url', '
> https://toolshed.g2.bx.psu.edu/'), ('name', 'fasta_formatter'), ('owner',
> 'devteam'), ('changeset_revision', '8f0ae92440b8'),
> ('latest_changeset_revision', '1dbb5181c327'), ('latest_ctx_rev', '1')]),
> 'tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=
> fasta_formatter&owner=devteam&changeset_revision=
> 8f0ae92440b8&latest_changeset_revision=1dbb5181c327&latest_ctx_rev=1')
> >   wsgi process: 'Multithreaded'
> > ------------------------------------------------------------
> >
> > Anything obvious that I've missed? Many thanks in advance for your help.
> > Kind regards,
> > Anne.
> > --
> > Dr Anne Pajon - Bioinformatics Core
> > Cancer Research UK - Cambridge Institute
> > Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
> > anne.pa...@cruk.cam.ac.uk | +44 (0)1223 769 631
> >
> > ___________________________________________________________
> > 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/
>
> --
> Dr Anne Pajon - Bioinformatics Core
> Cancer Research UK - Cambridge Institute
> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
> anne.pa...@cruk.cam.ac.uk | +44 (0)1223 769 631
>
>
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