On Thu Feb 05 2015 at 12:24:03 PM Anne Pajon <Anne.Pajon@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 <marten@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.Pajon@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=c6ca0ddb55be603a44ec9cad39b01202307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9'
> 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=c6ca0ddb55be603a44ec9cad39b01202307c62c9a25600e232d5d3d597344cb74ba4cd8a7123f6e9')
> 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.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
>
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--
Dr Anne Pajon - Bioinformatics Core
Cancer Research UK - Cambridge Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631