Ah, I think that I had a wrong impression before...so by default, the migration scripts listed here will NOT be executed, am I correct? I think that 'done' at the bottom made me think that it was executed...

So it's the user's responsibility to execute those scripts, correct?

Thanks,
Rui

The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed fromdatatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. Therepositories named emboss_5 and emboss_datatypes from the main Galaxy Tool Shed at http://toolshed.g2.bx.psu.eduwill be installed into your local Galaxy instance at the location discussed above by running the following command.

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
sh ./scripts/migrate_tools/0002_tools.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

done
After the installation process finishes, you can start your Galaxy server. As part of this installation process,entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so thesetools will continue to be loaded into your tool panel. Because of this, existing entries for these files should beremoved from your file named ./tool_conf.xml, but only after the installation process finishes.


On Wed, Aug 6, 2014 at 10:53 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Ahh, I think I see the issue.  So, many galaxy tools are being migrated out of the distribution and to the toolshed -- you can find much more detailed information here:  https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution

The samtools wrappers were migrated in migration 8, I think, if that helps.

Basically, there's a migration script that should have shown up in a terminal somewhere when you ran your galaxy instance after the update that will contain a reference to script(s) that you can run that'll take care of the migration.

Let me know if you need more information, if the wiki page doesn't clear it up!

-Dannon


On Wed, Aug 6, 2014 at 1:36 PM, Beginner TI <ruiwang.sz@gmail.com> wrote:
Hi Dannon,

Thanks for the reply. Sorry for the duplicate. I was wondering that the original subject sounded like a user problem so I updated it...

Actually we are having a little down time right now for a file system check. I'll try your suggestions asap and let you know. At the mean time, could you please elaborate this a little bit? I noticed that in the tool_conf.xml, not every tool is shown on the panel although they are all defined there in the same format. I also noticed that all the tool xml files, such as

<section id="samtools" name="NGS: SAM Tools">
    <tool file="samtools/sam_bitwise_flag_filter.xml" />
    <tool file="samtools/sam2interval.xml" />
    <tool file="samtools/sam_to_bam.xml" />
    <tool file="samtools/bam_to_sam.xml" />
    <tool file="samtools/sam_merge.xml" />
    <tool file="samtools/samtools_mpileup.xml" />
    <tool file="samtools/sam_pileup.xml" />
    <tool file="samtools/pileup_parser.xml" />
    <tool file="samtools/pileup_interval.xml" />
    <tool file="samtools/samtools_flagstat.xml" />
    <tool file="samtools/samtools_rmdup.xml" />
    <tool file="samtools/samtools_slice_bam.xml" />
  </section>

the directory samtools and all these xml files are no longer in the tools directory. seems that upgrade deleted them. is this correct? or they are moved to somewhere else? I looked around but didn't see. 

Based on this, I think that even I removed the tool_panel.xml file you mentioned, I will still not be able to restore samtools even I could see it...could you please let me know how I could configure this?

Thanks,
Rui


On Wed, Aug 6, 2014 at 10:23 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hi Rui,

We'll definitely take a look.  Please allow for a reasonable time period to pass before sending duplicate emails to the list asking for assistance.

That said, does deleting your integrated_tool_panel.xml (this file is automatically regenerated by Galaxy, safe to remove it and restart) bring back your manually installed samtools?


On Wed, Aug 6, 2014 at 1:08 PM, Beginner TI <ruiwang.sz@gmail.com> wrote:
Could someone please take a look?

Thanks,
Rui

On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI <ruiwang.sz@gmail.com> wrote:
Dear Admin,

Since the upgrade, I lost the samtools that I installed myself. Although it is still in the tool_conf.xml, it does not show up on the panel. I tried to install from toolshed, but failed. Error messages pasted below. Could someone take a look?

Thanks,
Rui

⇝ AttributeError: 'NoneType' object has no attribute 'strip'
URL: http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=d2c3034af88d998d&changeset_revisions=af65bfb54977
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__          view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__          view
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request          view
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:369 in decorator          view
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:983 in prepare_for_install          view
>>  includes_tool_dependencies )
Module tool_shed.util.common_install_util:97 in get_dependencies_for_repository          view
>>  repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name,repository_owner, changeset_revision )
Module tool_shed.util.shed_util_common:1036 in get_repository_for_dependency_relationship          view
>>  ( name, owner, changeset_revision ) )
Module tool_shed.util.shed_util_common:1867 in url_join          view
>>  parts.append( arg.strip( '/' ) )
AttributeError: 'NoneType' object has no attribute 'strip'



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