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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