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...@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.ba...@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...@gmail.com> wrote:
>>
>>> Could someone please take a look?
>>>
>>> Thanks,
>>> Rui
>>>
>>> On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI <ruiwang...@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
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> app_iter *=* self*.*application*(*environ*,* detect_start_response*)*
>>>> Module paste.recursive:*84* in __call__
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> *return* self*.*application*(*environ*,* start_response*)*
>>>> Module paste.httpexceptions:*633* in __call__
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> *return* self*.*application*(*environ*,* start_response*)*
>>>> Module galaxy.web.framework.base:*132* in __call__
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> *return* self*.*handle_request*(* environ*,* start_response *)*
>>>> Module galaxy.web.framework.base:*190* in handle_request
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> body *=* method*(* trans*,* ****kwargs *)*
>>>> Module galaxy.web.framework:*369* in decorator
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)*
>>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:*983* in
>>>> prepare_for_install
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> includes_tool_dependencies *)*
>>>> Module tool_shed.util.common_install_util:*97* in
>>>> get_dependencies_for_repository
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> 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
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> *(* name*,* owner*,* changeset_revision *)* *)*
>>>> Module tool_shed.util.shed_util_common:*1867* in url_join
>>>> <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#>
>>>>  view
>>>> <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#>
>>>> >>
>>>> <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#>
>>>> parts*.*append*(* arg*.*strip*(* '/' *)* *)*
>>>> *AttributeError: 'NoneType' object has no attribute 'strip'*
>>>>
>>>>
>>>
>>> ___________________________________________________________
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>>>
>>
>>
>
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