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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