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.vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvsh
./scripts/migrate_tools/0002_tools.sh^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^doneAfter
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.ba...@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...@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'*
>>>>>
>>>>>
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
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>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>>
>>
>
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