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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