Re: [galaxy-dev] ToolShed tool preview broken (TestToolShed too)

[Peter Cock]

On Wed, Oct 8, 2014 at 9:22 AM, Peter Cock  wrote:
> Hi all,
>
> From the "new tools" information Dave Compiled for the last Galaxy Update
> https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions
> I had a look at galaxyp's "filter_by_fasta_ids: Extract sequences from a
> FASTA file based on a list of IDs" tool:
>
> https://toolshed.g2.bx.psu.edu/view/galaxyp/filter_by_fasta_ids
>
> I wanted to see how it compared to my own similar tools (which handle
> FASTA, FASTQ, SFF and could  cover more - they replaced my older
> single format filter tools):
>
> https://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
> https://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
>
> Now for the bug report, clicking on the button (under valid tools) which
> would normally give a preview of the tool form is failing - giving just
> "Internal Server Error".
>
> I have tried a random selection of other tools and this seems to be
> universal - moreover the TestToolShed also seems to have
> the same problem.
>
> Regards,
>
> Peter

This is working again now.

See also another possibly related "Internal Server Error" on
upload which is also working again now:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-October/020619.html

Peter
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Re: [galaxy-dev] ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites'

[Peter Cock]

On Wed, Sep 10, 2014 at 7:55 PM, Nate Coraor  wrote:
> Hi Peter,
>
> This was due to a bug I introduced last week, which I've just fixed in
> d1f6d05. Sorry for the trouble.
>
> --nate

Thanks - I'll check back in a day or two once the tests have
run again.

Peter
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Re: [galaxy-dev] ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites'

[Nate Coraor]

Hi Peter,

This was due to a bug I introduced last week, which I've just fixed
in d1f6d05. Sorry for the trouble.

--nate

On Tue, Sep 9, 2014 at 9:50 AM, Peter Cock 
wrote:

> Hi all,
>
> I'm wondering why my samtools_depad repository tests have
> failed, and since I have not changed this recently presume this
> is due to a Galaxy change or general TestToolShed problem
> not specific to my tool:
>
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>
> Tests that failed
> Tool id: samtools_depad
> Tool version: samtools_depad
> Test: test_tool_00
> (
> functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1
> )
> Stderr:
> Traceback:
> Traceback (most recent call last):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 114, in test_tool
> self.do_it( td )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 35, in do_it
> self._verify_outputs( testdef, test_history, shed_tool_id,
> data_list, galaxy_interactor )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> line 75, in _verify_outputs
> galaxy_interactor.verify_output( history, output_data,
> output_testdef=output_testdef, shed_tool_id=shed_tool_id,
> maxseconds=maxseconds )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 82, in verify_output
> self._verify_metadata( history_id, hid, attributes )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> line 103, in _verify_metadata
> raise Exception( msg )
> Exception: Dataset metadata verification for [file_ext] failed,
> expected [bam] but found [None].
> Traceback (most recent call last):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/framework/decorators.py",
> line 243, in decorator
> rval = func( self, trans, *args, **kwargs)
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 188, in show
> return self.__show_dataset( trans, id, **kwd )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 214, in __show_dataset
> hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/base/controller.py",
> line 855, in get_display_apps
> for display_app in hda.get_display_applications( trans ).itervalues():
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/model/__init__.py",
> line 1754, in get_display_applications
> return self.datatype.get_display_applications_by_dataset( self, trans )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/data.py",
> line 445, in get_display_applications_by_dataset
> value = value.filter_by_dataset( dataset, trans )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py",
> line 200, in filter_by_dataset
> if link_value.filter_by_dataset( data, trans ):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py",
> line 78, in filter_by_dataset
> if fill_template( filter_elem.text, context = context ) !=
> filter_elem.get( 'value', 'True' ):
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/util/template.py",
> line 9, in fill_template
> return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
> return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1410263883_33_43576.py",
> line 82, in respond
> NotFound: cannot find 'ucsc_display_sites' while searching for
> 'APP.config.ucsc_display_sites'
> requests.packages.urllib3.connectionpool: DEBUG: "GET
>
> /api/histories/993bad2fe35335db/contents/7fbe67cfae825002?key=edc04240db9605fb7edc7bab44d3404c
> HTTP/1.1" 500 None
> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
> connection (1): 127.0.0.1
> requests.packages.urllib3.connectionpool: DEBUG: "GET
>
> /api/histories/993bad2fe353

Re: [galaxy-dev] ToolShed error: samtools installation failure

[Dannon Baker]

That's correct -- none of them are run automatically.


On Wed, Aug 6, 2014 at 3:08 PM, Beginner TI  wrote:

> 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.vsh 
> ./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 
> 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  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
>>>
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>   
>>>
>>> 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 
>>> 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 
 wrote:

> Could someone please take a look?
>
> Thanks,
> Rui
>
> On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI 
> 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
>> 

Re: [galaxy-dev] ToolShed error: samtools installation failure

[Beginner TI]

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.vsh
./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 
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  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
>>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>   
>>
>> 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 
>> 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 
>>> wrote:
>>>
 Could someone please take a look?

 Thanks,
 Rui

 On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI 
 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
> 
> >>
> 

Re: [galaxy-dev] ToolShed error: samtools installation failure

[Dannon Baker]

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  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
>
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   
>
> 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 
> 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  wrote:
>>
>>> Could someone please take a look?
>>>
>>> Thanks,
>>> Rui
>>>
>>> On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI 
>>> 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.ba

Re: [galaxy-dev] ToolShed error: samtools installation failure

[Beginner TI]

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














  

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 
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  wrote:
>
>> Could someone please take a look?
>>
>> Thanks,
>> Rui
>>
>> On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI  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
>>> 

Re: [galaxy-dev] ToolShed error: samtools installation failure

[Dannon Baker]

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  wrote:

> Could someone please take a look?
>
> Thanks,
> Rui
>
> On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI  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.control

Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

[Dooley, Damion]

That was it! Yay!  I'll add a Trello card to have this info gem added to the 
docs.

Thanks,

Damion

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

From: Aaron Petkau [aaron.pet...@gmail.com]
Sent: Friday, August 01, 2014 12:26 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure 
issue

Hmmm... you know what.  I tested this out and it looks like Galaxy expects the 
git repo to be named the same as the package name in your tool dependencies 
file ffp-phylogeny.  If you change the git command to:

git clone https://github.com/apetkau/ffp-3.19-custom.git ffp-phylogeny

I think it should work.

Aaron
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Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

[Aaron Petkau]

Hmmm... you know what.  I tested this out and it looks like Galaxy expects
the git repo to be named the same as the package name in your tool
dependencies file ffp-phylogeny.  If you change the git command to:

git clone https://github.com/apetkau/ffp-3.19-custom.git *ffp-phylogeny*

I think it should work.

Aaron


On Fri, Aug 1, 2014 at 2:09 PM, Dooley, Damion 
wrote:

> A little more info:
>
> ls -a
>
> #
> ls -a
> STDOUT
> .
> ..
> #
>
> #
> ls -a
> STDERR
>
> so I guess the .git archive is being unpackaged somewhere else!  After
> lunch I'll return to explore this mysterious territory.
>
> d.
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Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

[Dooley, Damion]

A little more info:

ls -a 

#
ls -a
STDOUT
.
..
#

#
ls -a
STDERR

so I guess the .git archive is being unpackaged somewhere else!  After lunch 
I'll return to explore this mysterious territory.

d. 
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Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

[Dooley, Damion]

Sadly,

 ./configure --disable-gui 
--prefix=$INSTALL_DIR

yeilds install error:

 /bin/sh: ./configure: No such file or directory

But file must be there since previous git step is carried out ok:
...
#
git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c
STDOUT
HEAD is now at 1819482 Added gitignore

#
git reset --hard 1819482db93bf0025c2588b5264cc0ec8c61029c
STDERR

#
./configure --disable-gui 
--prefix=/usr/local/galaxy/shared/tool_dependency/ffp-phylogeny/0.3.19_1819482db93bf0025c2588b5264cc0ec8c61029c/ddooley/ffp_phylogeny/4e213eee0fef
STDOUT

#
./configure --disable-gui 
--prefix=/usr/local/galaxy/shared/tool_dependency/ffp-phylogeny/0.3.19_1819482db93bf0025c2588b5264cc0ec8c61029c/ddooley/ffp_phylogeny/4e213eee0fef
STDERR
/bin/sh: ./configure: No such file or directory
#

argh!

d.

From: Aaron Petkau [aaron.pet...@gmail.com]
Sent: Friday, August 01, 2014 11:47 AM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure 
issue

Hey Damion,

You should be able to do ./configure --disable-gui ... to get it to work (that 
is, make sure the full path to the configure command is given).  At least I 
think that's probably what's going on.

Aaron


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Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue

[Aaron Petkau]

Hey Damion,

You should be able to do *./*configure --disable-gui ... to get it to work
(that is, make sure the full path to the configure command is given).  At
least I think that's probably what's going on.

Aaron


On Fri, Aug 1, 2014 at 12:32 PM, Dooley, Damion 
wrote:

> Hi folks,
>
> Having a difficult time with coding the "configure" step in this new
> tool_dependency.xml file, namely that an error "/bin/sh: configure: command
> not found" results when I try to install my beta development tool from a
> local test toolshed (which is downloading and installing other tools just
> fine).
>
> 
> git clone
> https://github.com/myuser/mygitstuff.git .
> git reset --hard
> 1819482db93bf0025c2588b5264cc0ec8c61029c
> configure --disable-gui
> --prefix=$INSTALL_DIR
> 
> 
> bin
>
> $INSTALL_DIR/bin
> 
> 
>  action="prepend_to">$INSTALL_DIR/bin
> 
> 
>
> Any hints about why this isn't being found or what the /bin/sh needs to
> get it going?
> When I do a git reset --hard, the "configure" file is definitely there,
> with executable flag set.  Any other permission oddities?
>
> I've also tried  , which yeilds same
> error.  (Skipping that line and doing 
> at least finds and runs "make", though it errors out for lack of input
> data).
>
> Regards,
>
> Damion
>
> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre
> for Disease Control
> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

[Greg Von Kuster]

I wasn't aware of a scenario where the value of dir could be None, so thanks 
for pointing this out.  It should be fixed in 14088:23f0c41b1cd7

Greg Von Kuster

On Jul 17, 2014, at 8:15 AM, Nicolas Lapalu  
wrote:

> Hi Greg,
> 
> not in the current, in version "2014-05-14", but I think the bug is still 
> there.
> 
> current version :
> 
> 83for action_tup in filtered_actions:
> 84current_dir = os.path.abspath( os.path.join( 
> work_dir, dir ) )
> 
> Fix:
> 
> 83for action_tup in filtered_actions:
> ..  if dir is None:
>   dir = ''
> 84current_dir = os.path.abspath( os.path.join( 
> work_dir, dir ) )
> 
> +
> nico
> 
> 
> Le 15/07/2014 20:41, Greg Von Kuster a écrit :
>> Are the problems described in this thread occurring with the latest Galaxy 
>> release?  The references to the code lines do not seem to reflect the latest 
>> Galaxy release.
>> 
>> Thanks,
>> 
>> Greg Von Kuster
>> 
>> On Jul 7, 2014, at 10:34 AM, Nicolas Lapalu 
>>  wrote:
>> 
>>> Hi
>>> 
>>> There's a bug in the 
>>> "galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py" file.
>>> line 79 : dir can be equal to None, but os.path.join() raises an error with 
>>> an arg equal to None
>>> To fix it :
>>> if dir == None:
>>>dir = ''
>>> 
>>> nico
>>> 
>>> Le 07/07/2014 14:38, Kandalaft, Iyad a écrit :
 That error sounds like it's trying to merge the current working directory 
 with the path supplied in the "CHMOD" tag.
  current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- 
 join work_dir with dir
 
 You have 2 possibilities to try:
 1. Eliminate the $INSTALLDIR from the path in the XML if you're already in 
 that path
 2. Changedir to the path before trying the CHMOD tag and use "." as the 
 path
 
 
 Iyad Kandalaft
 Microbial Biodiversity Bioinformatics
 Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
 960 Carling Ave.| 960 Ave. Carling
 Ottawa, ON| Ottawa (ON) K1A 0C6
 E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
 Telephone | Téléphone 613-759-1228
 Facsimile | Télécopieur 613-759-1701
 Teletypewriter | Téléimprimeur 613-773-2600
 Government of Canada | Gouvernement du Canada
 
 
 
 -Original Message-
 From: galaxy-dev-boun...@lists.bx.psu.edu 
 [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
 Sent: Monday, July 07, 2014 5:57 AM
 To: galaxy-dev@lists.bx.psu.edu
 Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem
 
 Hi all,
 
 I'm trying to package my tool wrapper to release it in the ToolShed. I 
 need to download the associated binary file and change the permissions.
 I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
 My tool_dependency_dir is well defined in my universe file. The download 
 is ok, but I get an error during the "chmod" action.
 So I tried with your example, faToTwoBit 
 (https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same 
 bug. Do you know the problem ? Do I need to configure someting else ?
 
 log :
 
 tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating 
 an existing record for version 0.0.1 of tool dependency faToTwoBit for 
 revision 5ac8ed26842c of repository mytool by updating the status from 
 Never installed to Installing.
 tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
 2014-07-07 11:28:34,374 Attempting to download from 
 http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
 127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST 
 /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
 "http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
 (X11; Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
 tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 
 Error installing tool dependency faToTwoBit version 0.0.1.
 Traceback (most recent call last):
File
 "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 110, in install_and_build_package_via_fabric
  tool_dependency = self.install_and_build_package( app, 
 tool_shed_repository, tool_dependency, actions_dict )
File
 "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
 line 79, in install_and_build_package
  current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
File "/usr/lib/python2.7/posixpath.py", line 75, in join
  if b.startswith('/'):
 AttributeError: 'NoneType' object has no attribute 'startswith'
 
 Thanks for your help;
 nico
 _

Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

[Nicolas Lapalu]

Hi Greg,

not in the current, in version "2014-05-14", but I think the bug is 
still there.


current version :

83for action_tup in filtered_actions:
84current_dir = os.path.abspath( os.path.join( 
work_dir, dir ) )


Fix:

83for action_tup in filtered_actions:
..  if dir is None:
   dir = ''
84current_dir = os.path.abspath( os.path.join( 
work_dir, dir ) )


+
nico


Le 15/07/2014 20:41, Greg Von Kuster a écrit :

Are the problems described in this thread occurring with the latest Galaxy 
release?  The references to the code lines do not seem to reflect the latest 
Galaxy release.

Thanks,

Greg Von Kuster

On Jul 7, 2014, at 10:34 AM, Nicolas Lapalu  
wrote:


Hi

There's a bug in the 
"galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py" file.
line 79 : dir can be equal to None, but os.path.join() raises an error with an 
arg equal to None
To fix it :
if dir == None:
dir = ''

nico

Le 07/07/2014 14:38, Kandalaft, Iyad a écrit :

That error sounds like it's trying to merge the current working directory with the path 
supplied in the "CHMOD" tag.
  current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- join 
work_dir with dir

You have 2 possibilities to try:
1. Eliminate the $INSTALLDIR from the path in the XML if you're already in that 
path
2. Changedir to the path before trying the CHMOD tag and use "." as the path


Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada



-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
Sent: Monday, July 07, 2014 5:57 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem

Hi all,

I'm trying to package my tool wrapper to release it in the ToolShed. I need to 
download the associated binary file and change the permissions.
I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
My tool_dependency_dir is well defined in my universe file. The download is ok, but I get 
an error during the "chmod" action.
So I tried with your example, faToTwoBit 
(https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same bug. 
Do you know the problem ? Do I need to configure someting else ?

log :

tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating an 
existing record for version 0.0.1 of tool dependency faToTwoBit for revision 
5ac8ed26842c of repository mytool by updating the status from Never installed 
to Installing.
tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
2014-07-07 11:28:34,374 Attempting to download from 
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST /admin_toolshed/repository_installation_status_updates 
HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
(X11; Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 Error 
installing tool dependency faToTwoBit version 0.0.1.
Traceback (most recent call last):
File
"/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 110, in install_and_build_package_via_fabric
  tool_dependency = self.install_and_build_package( app, 
tool_shed_repository, tool_dependency, actions_dict )
File
"/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 79, in install_and_build_package
  current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
File "/usr/lib/python2.7/posixpath.py", line 75, in join
  if b.startswith('/'):
AttributeError: 'NoneType' object has no attribute 'startswith'

Thanks for your help;
nico
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Re: [galaxy-dev] Toolshed roadmap

[Greg Von Kuster]

Hello Eric,

The Tool Shed wiki is currently undergoing significant changes which will 
hopefully result in an improved set of documentation.  This is a high priority 
between now and October ( see 
https://trello.com/c/Gg0jnll7/191-wiki-improvements and 
https://trello.com/c/uHyAaCLT/176-tasks-for-completion-by-october-2014).

In the meantime, you may find my blog posts to be helpful ( see 
http://gregvonkuster.org )

Greg Von Kuster

On Jul 15, 2014, at 4:00 PM, Eric Rasche  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Hi Greg,
> 
> Sorry about that, toolshed development hasn't been very visible in my
> view of galaxy thus far, so it seemed like asking someone who knew would
> be the fastest route here. I'll ensure my future inquires go to galaxy-dev.
> 
> On 07/15/2014 02:18 PM, Greg Von Kuster wrote:
>> Hello Eric,
>> 
>> Please use Biostar or the Galaxy dev mail list rather than individual email 
>> addresses in order to ensure faster responses.  Pleasse see my responses 
>> below.
>> 
>> On Jul 14, 2014, at 10:20 AM, Eric Rasche  wrote:
>> 
>> Howdy Greg,
>> 
>> Since there isn't really a public/published roadmap and you're the
>> toolshed guy, I'm emailing to see if I can find out what's in the
>> toolshed's future.
>> 
>>> The tool shed Trello board at 
>>> https://trello.com/b/vHqpKpZF/galaxy-tool-shed is the roadmap for the Tool 
>>> Shed.  Just like the Galaxy Development Trello board, you should be able to 
>>> add new cards to the Inbox, and vote on existing cards to raise their 
>>> priority.  Please let us know if you are not able to do these things.
> 
> I was not aware that a trello board even existed for the toolshed, that
> would have answered some of these.
> 
> (It might be good to have it mentioned more than once on the wiki,
> perhaps under "Toolshed" and not just under "Issues")
> 
>> Specifically, I'm wondering if there will be API calls for the following
>> things:
>> 
>> - creating repositories
>> 
>>> I've added the following Trello card for the above feature.  However, it is 
>>> currently possible to create new repositories via the API by importing a 
>>> repository capsule (i.e., ~/api/repositories/import_capsule).
>> 
>>> https://trello.com/c/cUUWeBCi/234-enhance-the-api-to-enable-creation-of-new-repositories
>> 
>> - obtaining a list of categories
>> 
>>> The above was introduced in the June 2, 2014 release, so, for example, the 
>>> following will work.
>> 
>>> https://testtoolshed.g2.bx.psu.edu/api/categories
> 
> Are any of these API changes documented outside of
> mercurial/DevNewsBriefs (trello)?
> 
> My go-to locations for documentation are the wiki and readthedocs.
> 
> Neither https://wiki.galaxyproject.org/ToolShedApi
> or
> http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.tool_shed.api.html
> 
> has up-to-date documentation. Is there another place I should be looking
> for static, complete toolshed API information?
> 
>> - obtaining category information within the /api/repositories call
>> 
>>> I've added the following Trello card for this feature.
>> 
>>> https://trello.com/c/n7P0GE1P/235-enhance-the-api-repositories-feature
> 
> Thanks!
> 
>> 
>> 
>> 
>> Cheers,
>> Eric
>> 
>> 
> 
> Cheers,
> Eric
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Re: [galaxy-dev] Toolshed roadmap

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Greg,

Sorry about that, toolshed development hasn't been very visible in my
view of galaxy thus far, so it seemed like asking someone who knew would
be the fastest route here. I'll ensure my future inquires go to galaxy-dev.

On 07/15/2014 02:18 PM, Greg Von Kuster wrote:
> Hello Eric,
> 
> Please use Biostar or the Galaxy dev mail list rather than individual email 
> addresses in order to ensure faster responses.  Pleasse see my responses 
> below.
> 
> On Jul 14, 2014, at 10:20 AM, Eric Rasche  wrote:
> 
> Howdy Greg,
> 
> Since there isn't really a public/published roadmap and you're the
> toolshed guy, I'm emailing to see if I can find out what's in the
> toolshed's future.
> 
>> The tool shed Trello board at https://trello.com/b/vHqpKpZF/galaxy-tool-shed 
>> is the roadmap for the Tool Shed.  Just like the Galaxy Development Trello 
>> board, you should be able to add new cards to the Inbox, and vote on 
>> existing cards to raise their priority.  Please let us know if you are not 
>> able to do these things.

I was not aware that a trello board even existed for the toolshed, that
would have answered some of these.

(It might be good to have it mentioned more than once on the wiki,
perhaps under "Toolshed" and not just under "Issues")

> Specifically, I'm wondering if there will be API calls for the following
> things:
> 
> - creating repositories
> 
>> I've added the following Trello card for the above feature.  However, it is 
>> currently possible to create new repositories via the API by importing a 
>> repository capsule (i.e., ~/api/repositories/import_capsule).
> 
>> https://trello.com/c/cUUWeBCi/234-enhance-the-api-to-enable-creation-of-new-repositories
> 
> - obtaining a list of categories
> 
>> The above was introduced in the June 2, 2014 release, so, for example, the 
>> following will work.
> 
>> https://testtoolshed.g2.bx.psu.edu/api/categories

Are any of these API changes documented outside of
mercurial/DevNewsBriefs (trello)?

My go-to locations for documentation are the wiki and readthedocs.

Neither https://wiki.galaxyproject.org/ToolShedApi
or
http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.tool_shed.api.html

has up-to-date documentation. Is there another place I should be looking
for static, complete toolshed API information?

> - obtaining category information within the /api/repositories call
> 
>> I've added the following Trello card for this feature.
> 
>> https://trello.com/c/n7P0GE1P/235-enhance-the-api-repositories-feature

Thanks!

> 
> 
> 
> Cheers,
> Eric
> 
> 

Cheers,
Eric
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Re: [galaxy-dev] Toolshed roadmap

[Greg Von Kuster]

Hello Eric,

Please use Biostar or the Galaxy dev mail list rather than individual email 
addresses in order to ensure faster responses.  Pleasse see my responses below.

On Jul 14, 2014, at 10:20 AM, Eric Rasche  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Howdy Greg,
> 
> Since there isn't really a public/published roadmap and you're the
> toolshed guy, I'm emailing to see if I can find out what's in the
> toolshed's future.

The tool shed Trello board at https://trello.com/b/vHqpKpZF/galaxy-tool-shed is 
the roadmap for the Tool Shed.  Just like the Galaxy Development Trello board, 
you should be able to add new cards to the Inbox, and vote on existing cards to 
raise their priority.  Please let us know if you are not able to do these 
things.

> 
> Specifically, I'm wondering if there will be API calls for the following
> things:
> 
> - - creating repositories

I've added the following Trello card for the above feature.  However, it is 
currently possible to create new repositories via the API by importing a 
repository capsule (i.e., ~/api/repositories/import_capsule).

https://trello.com/c/cUUWeBCi/234-enhance-the-api-to-enable-creation-of-new-repositories


> - - obtaining a list of categories

The above was introduced in the June 2, 2014 release, so, for example, the 
following will work.

https://testtoolshed.g2.bx.psu.edu/api/categories


> - - obtaining category information within the /api/repositories call

I've added the following Trello card for this feature.

https://trello.com/c/n7P0GE1P/235-enhance-the-api-repositories-feature


> 
> Cheers,
> Eric
> 
> - -- 
> Eric Rasche
> Programmer II
> Center for Phage Technology
> Texas A&M University
> College Station, TX 77843
> 404-692-2048
> e...@tamu.edu
> rasche.e...@yandex.ru
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Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

[Greg Von Kuster]

Are the problems described in this thread occurring with the latest Galaxy 
release?  The references to the code lines do not seem to reflect the latest 
Galaxy release.

Thanks,

Greg Von Kuster

On Jul 7, 2014, at 10:34 AM, Nicolas Lapalu  
wrote:

> Hi
> 
> There's a bug in the 
> "galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py" file.
> line 79 : dir can be equal to None, but os.path.join() raises an error with 
> an arg equal to None
> To fix it :
> if dir == None:
>dir = ''
> 
> nico
> 
> Le 07/07/2014 14:38, Kandalaft, Iyad a écrit :
>> That error sounds like it's trying to merge the current working directory 
>> with the path supplied in the "CHMOD" tag.
>>  current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- join 
>> work_dir with dir
>> 
>> You have 2 possibilities to try:
>> 1. Eliminate the $INSTALLDIR from the path in the XML if you're already in 
>> that path
>> 2. Changedir to the path before trying the CHMOD tag and use "." as the path
>> 
>> 
>> Iyad Kandalaft
>> Microbial Biodiversity Bioinformatics
>> Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
>> 960 Carling Ave.| 960 Ave. Carling
>> Ottawa, ON| Ottawa (ON) K1A 0C6
>> E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
>> Telephone | Téléphone 613-759-1228
>> Facsimile | Télécopieur 613-759-1701
>> Teletypewriter | Téléimprimeur 613-773-2600
>> Government of Canada | Gouvernement du Canada
>> 
>> 
>> 
>> -Original Message-
>> From: galaxy-dev-boun...@lists.bx.psu.edu 
>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
>> Sent: Monday, July 07, 2014 5:57 AM
>> To: galaxy-dev@lists.bx.psu.edu
>> Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem
>> 
>> Hi all,
>> 
>> I'm trying to package my tool wrapper to release it in the ToolShed. I need 
>> to download the associated binary file and change the permissions.
>> I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
>> My tool_dependency_dir is well defined in my universe file. The download is 
>> ok, but I get an error during the "chmod" action.
>> So I tried with your example, faToTwoBit 
>> (https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same 
>> bug. Do you know the problem ? Do I need to configure someting else ?
>> 
>> log :
>> 
>> tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating 
>> an existing record for version 0.0.1 of tool dependency faToTwoBit for 
>> revision 5ac8ed26842c of repository mytool by updating the status from Never 
>> installed to Installing.
>> tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
>> 2014-07-07 11:28:34,374 Attempting to download from 
>> http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
>> 127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST 
>> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
>> "http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
>> (X11; Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
>> tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 Error 
>> installing tool dependency faToTwoBit version 0.0.1.
>> Traceback (most recent call last):
>>File
>> "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>> line 110, in install_and_build_package_via_fabric
>>  tool_dependency = self.install_and_build_package( app, 
>> tool_shed_repository, tool_dependency, actions_dict )
>>File
>> "/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
>> line 79, in install_and_build_package
>>  current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
>>File "/usr/lib/python2.7/posixpath.py", line 75, in join
>>  if b.startswith('/'):
>> AttributeError: 'NoneType' object has no attribute 'startswith'
>> 
>> Thanks for your help;
>> nico
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this and other Galaxy 
>> lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>> 
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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> 


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To search G

Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

[Nicolas Lapalu]

Hi

There's a bug in the 
"galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py" file.
line 79 : dir can be equal to None, but os.path.join() raises an error 
with an arg equal to None

To fix it :
if dir == None:
dir = ''

nico

Le 07/07/2014 14:38, Kandalaft, Iyad a écrit :

That error sounds like it's trying to merge the current working directory with the path 
supplied in the "CHMOD" tag.
  current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- join 
work_dir with dir

You have 2 possibilities to try:
1. Eliminate the $INSTALLDIR from the path in the XML if you're already in that 
path
2. Changedir to the path before trying the CHMOD tag and use "." as the path


Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada



-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
Sent: Monday, July 07, 2014 5:57 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem

Hi all,

I'm trying to package my tool wrapper to release it in the ToolShed. I need to 
download the associated binary file and change the permissions.
I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
My tool_dependency_dir is well defined in my universe file. The download is ok, but I get 
an error during the "chmod" action.
So I tried with your example, faToTwoBit 
(https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same bug. 
Do you know the problem ? Do I need to configure someting else ?

log :

tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating an 
existing record for version 0.0.1 of tool dependency faToTwoBit for revision 
5ac8ed26842c of repository mytool by updating the status from Never installed 
to Installing.
tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
2014-07-07 11:28:34,374 Attempting to download from 
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST /admin_toolshed/repository_installation_status_updates 
HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
(X11; Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 Error 
installing tool dependency faToTwoBit version 0.0.1.
Traceback (most recent call last):
File
"/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 110, in install_and_build_package_via_fabric
  tool_dependency = self.install_and_build_package( app, 
tool_shed_repository, tool_dependency, actions_dict )
File
"/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 79, in install_and_build_package
  current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
File "/usr/lib/python2.7/posixpath.py", line 75, in join
  if b.startswith('/'):
AttributeError: 'NoneType' object has no attribute 'startswith'

Thanks for your help;
nico
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Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

[Kandalaft, Iyad]

That error sounds like it's trying to merge the current working directory with 
the path supplied in the "CHMOD" tag.
 current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) <-- join 
work_dir with dir

You have 2 possibilities to try:
1. Eliminate the $INSTALLDIR from the path in the XML if you're already in that 
path
2. Changedir to the path before trying the CHMOD tag and use "." as the path


Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada 



-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nicolas Lapalu
Sent: Monday, July 07, 2014 5:57 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Toolshed : tool_dependency xml, action problem

Hi all,

I'm trying to package my tool wrapper to release it in the ToolShed. I need to 
download the associated binary file and change the permissions. 
I wrote a tool_dependency xml file with a downlod_binary and chmod actions.
My tool_dependency_dir is well defined in my universe file. The download is ok, 
but I get an error during the "chmod" action.
So I tried with your example, faToTwoBit 
(https://wiki.galaxyproject.org/DownloadingBinaries), and I get the same bug. 
Do you know the problem ? Do I need to configure someting else ?

log :

tool_shed.util.tool_dependency_util DEBUG 2014-07-07 11:28:34,346 Updating an 
existing record for version 0.0.1 of tool dependency faToTwoBit for revision 
5ac8ed26842c of repository mytool by updating the status from Never installed 
to Installing.
tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG
2014-07-07 11:28:34,374 Attempting to download from 
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit to bin
127.0.0.1 - - [07/Jul/2014:11:28:36 +0200] "POST 
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
"http://127.0.0.1:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 (X11; 
Linux x86_64; rv:24.0) Gecko/20140610 Firefox/24.0 Iceweasel/24.6.0"
tool_shed.galaxy_install.install_manager ERROR 2014-07-07 11:28:39,038 Error 
installing tool dependency faToTwoBit version 0.0.1.
Traceback (most recent call last):
   File
"/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 110, in install_and_build_package_via_fabric
 tool_dependency = self.install_and_build_package( app, 
tool_shed_repository, tool_dependency, actions_dict )
   File
"/home/nlapalu/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py",
line 79, in install_and_build_package
 current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
   File "/usr/lib/python2.7/posixpath.py", line 75, in join
 if b.startswith('/'):
AttributeError: 'NoneType' object has no attribute 'startswith'

Thanks for your help;
nico
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Re: [galaxy-dev] Toolshed upload error message

[Dave Bouvier]

Vipin,

I've attempted to duplicate this error locally, with no luck as yet. 
Would you be able to send me the specific tar.gz file that was causing 
problems?


  --Dave B.

On Wed 11 Jun 2014 05:02:34 PM EDT, Vipin TS wrote:

Hi Greg,

Please find the attached screenshot from my side. The same screen
message displayed yesterday.

I can see that the new revision number updated at repository page. I
tried to clone the repository and
which returns a empty folder.

When I click on the new revision number, I can see the commit message
displayed and when
click on the browse button from the left side which essentially gives
a blank page. (screenshot attached)

But when I view the "content of this repository" from the repository
page it seems the files are updated. (screenshot attached)
I selected the root folders correctly. I am not sure what is wrong
here. Could you please have a look on this.

Many thanks,
Vipin | Rätsch Lab


On Wed, Jun 11, 2014 at 9:03 AM, Greg Von Kuster mailto:g...@bx.psu.edu>> wrote:

Hi Vipin,

Can you elaborate on the error you are seeing?

Thanks,

Greg Von Kuster

On Jun 10, 2014, at 8:07 PM, Vipin TS mailto:vipin...@gmail.com>> wrote:


Hi Greg,

When I trying to upload a next release version o my
https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf
converter program to Community Toolshed, I am getting an internal
error message.

I am uploading a tar.gz file to the page
https://toolshed.g2.bx.psu.edu/ but this fails.

Could you please pass the error message or let me how I can add
new files to the repository and delete the old version.

Thanks,

Vipin | Rätsch Lab
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Re: [galaxy-dev] Toolshed upload error message

[Greg Von Kuster]

Hi Vipin,

Can you elaborate on the error you are seeing?

Thanks,

Greg Von Kuster

On Jun 10, 2014, at 8:07 PM, Vipin TS  wrote:

> Hi Greg, 
> 
> When I trying to upload a next release version o my 
> https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter program 
> to Community Toolshed, I am getting an internal error message. 
> 
> I am uploading a tar.gz file to the page https://toolshed.g2.bx.psu.edu/ but 
> this fails. 
> 
> Could you please pass the error message or let me how I can add new files to 
> the repository and delete the old version. 
> 
> Thanks, 
> 
> Vipin | Rätsch Lab
> ___
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Re: [galaxy-dev] Toolshed update list?

[Greg Von Kuster]

Hello Eric,

For repositories in the Tool Shed itself, there is no feature to formally track 
updates to repositories.  For repositories installed from a Tool Shed inot a 
Galaxy instance, the "Manage installed tool shed repositories" page includes a 
feature to discover updates availabe for all installed repositories.

Can you describe further what you need for the Tool Shed, if you are not 
referring to installed repositories?  A Tool Shed centric featue like this 
would need to provide a time frame in which repositories were updated, 
something like a start time and an end time, ot mark the repository somehow and 
determine whethere an update has been made to the repository since it was 
marked.

Is this what you are looking for?

Thanks,

Greg Von Kuster

On Jun 10, 2014, at 12:39 PM, Eric Rasche  wrote:

> Is there any way to access a list of repository updates in a toolshed, 
> perhaps as an RSS feed? Alternatively, is this data available internally and 
> it just requires writing a route to handle that query?
> 
> As of now when I log into my toolshed I'm faced with a page of meaningless 
> hashes and version numbers which I cannot mentally track for updates across 
> multiple days/projects.
> 
> Cheers,
> Eric
> 
> -- 
> Eric Rasche
> Programmer II
> Center for Phage Technology
> Texas A&M University
> College Station, TX 77843
> 404-692-2048
> e...@tamu.edu
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Re: [galaxy-dev] ToolShed for Visualisation Registry?

[John Chilton]

Hello Saket,

Thanks for your interest - I totally agree, I think a lot of tools
like this would be better served as visualization plugins. There is a
Trello card for this request https://trello.com/c/YLA70rZx - please
vote up if you are interested.

This has been discussed by the core team and I some member of the team
was largely in favor though there was some descent. I think both the
tool shed and visualization framework are well suited to allow this
integration (not that there aren't many little hurdles, but I think at
a high level it should be possible).

That said - I don't think this is a top priority for the core team
right now (though others should definitely correct me if I am wrong) -
and I would be surprised to see movement on it this year.

Perhaps until this is available perhaps the community should just
maintain a centralized list of repositories on the wiki? I think
seeing a list of community developed plugins would also help the team
guage how important automating install of new plugins should be.

-John





On Fri, Jun 6, 2014 at 8:43 AM, Saket Choudhary  wrote:
> I was wondering if there is a possibility of a 'Tool'Shed for
> Visualisation registry plugins(custom plugins, developed by
> users/developers)?
>
> The motivation for this comes from a small 'tool' I wrote for
> visualiing fastq phred scores using box plots[Still under development]
> here:
> http://saketkc.github.io/biojs/src/test/javascript/TestPhredScoreViewer.html
>
> I am relying on d3.text to read my fastq, but I believe I could handle
> this in a much better way had I written it for Galaxy's Visualisation
> registry specifically. For e.g. I could fetch
> fastq scores line by line using Galaxy's API, which would make my task
> a bit easier.
>
> I could always keep this to my local instance of Galaxy, but a
> 'toolshed' or 'registry' for visualisation  would help.
>
>
> Saket
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Re: [galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files

[Peter Cock]

On Tue, May 27, 2014 at 4:15 PM, Greg Von Kuster  wrote:
> Hello Peter,
>
> This issue should be resolved in 13630:33b1ff4b9985, which is now running on 
> the test Tool Shed.  Thanks for reporting this!
>
> Greg Von Kuster

Thanks - clearer error messages are a good thing :)

Peter
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Re: [galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files

[Greg Von Kuster]

Hello Peter,

This issue should be resolved in 13630:33b1ff4b9985, which is now running on 
the test Tool Shed.  Thanks for reporting this!

Greg Von Kuster

On May 19, 2014, at 1:41 PM, Peter Cock  wrote:

> Hi Greg, Dave,
> 
> I just tried to upload an updated tar-ball to the Test ToolShed and
> got a red error message:
> 
> 
> Uploaded archives can only include regular directories and files (no
> symbolic links, devices, etc). Offender:
> 
> 
> Note no offending files were listed. When I double checked I had prepared
> my tar-ball from the wrong source directory and it did contain symlinks, but
> the Tool Shed error message failed to list these.
> 
> Regards,
> 
> Peter
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Re: [galaxy-dev] ToolShed slow? esp uploading

[Peter Cock]

On Tue, Jan 21, 2014 at 6:19 PM, Peter Cock  wrote:
> Hi guys,
>
> I'm currently trying to update the blast_datatypes on the main
> tool shed (thanks Nicola for the reminder),
> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>
> Having clicked "upload" it is stuck at:
>
> "[Warning] Upload a single file or tarball. Uploading may take a while,
> depending upon the size of the file. Wait until a message is displayed
> in your browser after clicking the Upload button below."
>
> At what point do I give up and retry? Its been 8 minutes since
> I thought to start timing, call it 10 minutes so far...

I gave up after ~20 minutes, closed that tab, and tried again.
It worked perfectly twice in a row (blast_datatypes v0.0.17
and v0.0.18).

Peter
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Re: [galaxy-dev] toolshed image file location problem

[Eric Kuyt]

Ok thanks, I will vote it up, and for now try to manually edit
lib/tool_shed/util/shed_util_common.py

Thanks

On 20 January 2014 15:51, Bjoern Gruening  wrote:
> Hi Eric,
>
> please see the following ticket for it and vote it up :)
>
> https://trello.com/c/dWvkfBKC
>
> Sorry that there is no fix for it yet,
> Bjoern
>
>
>> e the actual image is located at
>
>
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Re: [galaxy-dev] Toolshed throwing error when reading tool's XML

[Greg Von Kuster]

It's discussed in the following page of the Tool Shed wiki.

https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance


On Jan 20, 2014, at 7:27 PM, "Dooley, Damion"  wrote:

> That advice did the trick, thanks Greg.  I only had .loc files in the upload 
> set; didn't know about the .sample version or 
> tool_data_table_conf.xml.sample.  One thing, did I miss reading the 
> documentation on this somewhere or is this workshop type knowledge?
> 
> From: Greg Von Kuster [g...@bx.psu.edu]
> Sent: Monday, January 20, 2014 1:21 PM
> To: Dooley, Damion
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Toolshed throwing error when reading tool's XML
> 
> Hello Damion,
> 
> Tool Shed repositories that contain tools that include dynamically generated 
> select list parameters that refer to an entry in the tool_data_table_conf.xml 
> file must contain a tool_data_table_conf.xml.sample file that contains the 
> required entry for each dynamic parameter. Similarly, any index files (i.e., 
> ~/tool-data/xxx.loc files) to which the tool_data_table_conf.xml file entries 
> refer must be defined in xxx.loc.sample files included in the tool shed 
> repository along with the tools. If any of these tool_data_table_conf.xml 
> entries or any of the required xxx.loc.sample files are missing from the tool 
> shed repository, the tools will not properly load and metadata will not be 
> generated for the repository. This means that the tools cannot be 
> automatically installed into a Galaxy instance.
> 
> For those tools that include dynamically generated select list parameters 
> that require a missing entry in the tool_data_table_conf.xml file, this file 
> will be modified in real time (when it is installed into a Galaxy instance) 
> by adding the entry from a tool_data_table_conf.xml.sample file contained in 
> the tool shed repository.
> 
> Based on your problem description, it seems that your repository may not 
> include a required xxx.loc.sample file.
> 
> Let me know if adding one does not solve the problem.  Is your repository in 
> one of the Galaxy team;'s public tool sheds?
> 
> Greg Von Kuster
> 


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Re: [galaxy-dev] Toolshed throwing error when reading tool's XML

[Dooley, Damion]

That advice did the trick, thanks Greg.  I only had .loc files in the upload 
set; didn't know about the .sample version or tool_data_table_conf.xml.sample.  
One thing, did I miss reading the documentation on this somewhere or is this 
workshop type knowledge?

From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Monday, January 20, 2014 1:21 PM
To: Dooley, Damion
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Toolshed throwing error when reading tool's XML

Hello Damion,

Tool Shed repositories that contain tools that include dynamically generated 
select list parameters that refer to an entry in the tool_data_table_conf.xml 
file must contain a tool_data_table_conf.xml.sample file that contains the 
required entry for each dynamic parameter. Similarly, any index files (i.e., 
~/tool-data/xxx.loc files) to which the tool_data_table_conf.xml file entries 
refer must be defined in xxx.loc.sample files included in the tool shed 
repository along with the tools. If any of these tool_data_table_conf.xml 
entries or any of the required xxx.loc.sample files are missing from the tool 
shed repository, the tools will not properly load and metadata will not be 
generated for the repository. This means that the tools cannot be automatically 
installed into a Galaxy instance.

For those tools that include dynamically generated select list parameters that 
require a missing entry in the tool_data_table_conf.xml file, this file will be 
modified in real time (when it is installed into a Galaxy instance) by adding 
the entry from a tool_data_table_conf.xml.sample file contained in the tool 
shed repository.

Based on your problem description, it seems that your repository may not 
include a required xxx.loc.sample file.

Let me know if adding one does not solve the problem.  Is your repository in 
one of the Galaxy team;'s public tool sheds?

Greg Von Kuster

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Re: [galaxy-dev] Toolshed throwing error when reading tool's XML

[Greg Von Kuster]

Hello Damion,
Tool Shed repositories that contain tools that include dynamically generated 
select list parameters that refer to an entry in the tool_data_table_conf.xml 
file must contain a tool_data_table_conf.xml.sample file that contains the 
required entry for each dynamic parameter. Similarly, any index files (i.e., 
~/tool-data/xxx.loc files) to which the tool_data_table_conf.xml file entries 
refer must be defined in xxx.loc.sample files included in the tool shed 
repository along with the tools. If any of these tool_data_table_conf.xml 
entries or any of the required xxx.loc.sample files are missing from the tool 
shed repository, the tools will not properly load and metadata will not be 
generated for the repository. This means that the tools cannot be automatically 
installed into a Galaxy instance.

For those tools that include dynamically generated select list parameters that 
require a missing entry in the tool_data_table_conf.xml file, this file will be 
modified in real time (when it is installed into a Galaxy instance) by adding 
the entry from a tool_data_table_conf.xml.sample file contained in the tool 
shed repository.

Based on your problem description, it seems that your repository may not 
include a required xxx.loc.sample file.

Let me know if adding one does not solve the problem.  Is your repository in 
one of the Galaxy team;'s public tool sheds?

Greg Von Kuster



On Jan 20, 2014, at 2:24 PM, "Dooley, Damion"  wrote:

> I'm stumped: Can tools that are destined for the toolshed use  from_data_table="..." ...> ?
> 
> In a blast_reporting.xml tool script I have
> 
>   
>   
>column="type" />
>   
>   
>   
> 
> But when this gets submitted as a tar file into a toolshed repository, 
> toolshed comes back with cryptic:
> 
> Metadata may have been defined for some items in revision '5bbb25b32de2'. 
> Correct the following problems if necessary and reset metadata.
> blast_reporting.xml - invalid literal for int() with base 10: 'type'
> 
> I eliminate the  
> line, but similar problem is still reported 
> 
> blast_reporting.xml - invalid literal for int() with base 10: 'name'
> 
> This hints that maybe the toolshed, when it tests the code, it doesn't know 
> what/where blast_reporting_fields is?  Is there some special location that 
> the blast_reporting_fields.loc file should be located within the uploaded tar 
> file?  (I tried putting it in various relative paths in the tar file, i.e. 
> root, and under /tool-data/)
> 
> p.s. the tool runs file with menu functioning in galaxy itself.
> 
> Thanks for any pro tips you folks can come up with!
> 
> Damion
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Re: [galaxy-dev] toolshed image file location problem

[Bjoern Gruening]

Hi Eric,

please see the following ticket for it and vote it up :)

https://trello.com/c/dWvkfBKC

Sorry that there is no fix for it yet,
Bjoern


> e the actual image is located at


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Re: [galaxy-dev] toolshed error on cloudman

[Björn Grüning]

Hi Karen,

that bug was fixed. Can you update your Galaxy installation?

Cheers,
Bjoern

> Hello, 
> 
> 
> I am currently unable to install a number of tools from toolshed to
> our cloud instance.  Unfortunately, this pops up for quite a few tools
> (I am currently trying to install cuffmerge, but I see this again and
> again).  Any help would be appreciated!
> 
> 
> I am seeing the following error:
> 
> 
> URL: 
> http://ec2-54-204-115-185.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=1a0e2ec172f34c67&changeset_revisions=a29a35968ddb
> File
> '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File
> '/mnt/galaxy/galaxy-app/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', 
> line 84 in __call__
>   return self.application(environ, start_response)
> File
> '/mnt/galaxy/galaxy-app/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>  line 633 in __call__
>   return self.application(environ, start_response)
> File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/base.py', line
> 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/base.py', line
> 190 in handle_request
>   body = method( trans, **kwargs )
> File '/mnt/galaxy/galaxy-app/lib/galaxy/web/framework/__init__.py',
> line 221 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/mnt/galaxy/galaxy-app/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>  line 896 in prepare_for_install
>   common_install_util.get_dependencies_for_repository( trans,
> tool_shed_url, repo_info_dict, includes_tool_dependencies )
> File
> '/mnt/galaxy/galaxy-app/lib/tool_shed/util/common_install_util.py',
> line 84 in get_dependencies_for_repository
>   installed_rd, missing_rd =
> get_installed_and_missing_repository_dependencies_for_new_install( trans, 
> repo_info_tuple )
> File
> '/mnt/galaxy/galaxy-app/lib/tool_shed/util/common_install_util.py',
> line 190 in
> get_installed_and_missing_repository_dependencies_for_new_install
>   tool_shed, name, owner, changeset_revision,
> prior_installation_required =
> suc.parse_repository_dependency_tuple( rd_tup )
> File '/mnt/galaxy/galaxy-app/lib/tool_shed/util/shed_util_common.py',
> line 1106 in parse_repository_dependency_tuple
>   prior_installation_required = str( prior_installation_required )
> UnboundLocalError: local variable 'prior_installation_required'
> referenced before assignment
> 
> 
> -- 
> Karen H. Miga, PhD
> 
> Postdoctoral Scholar
> University of California, Santa Cruz
> (831)459-5232
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Re: [galaxy-dev] toolshed contact not working (varscan)

[John Chilton]

Hey Geert,

  Very sorry about that. I broke the tool shed e-mail functionality. I
committed a fix and Dave pushed it out and now it seems to be working
again. Thanks for reporting the problem.

-John

On Fri, Oct 25, 2013 at 7:26 AM, Geert Vandeweyer
 wrote:
> Hi,
>
> I tried to contact the owner of the varscan repository through the main
> toolshed ( http://toolshed.g2.bx.psu.edu/) "repository actions, contact
> owner function. Upon submission I got the following error :
>
> An error occurred sending your message by email: 'Configuration' object has
> no attribute 'smtp_ssl'
> Is this a known issue? The option is not available if I browse the
> repository from my local galaxy admin pages.
>
> In case fcaramia reads this, please contact me, I have some updates to your
> varscan somatics script, as the default scripts failed to run for me.
>
> Best,
>
> Geert
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
>
>
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Re: [galaxy-dev] Toolshed reset all repository metadata

[Greg Von Kuster]

Hello Simon,


On Oct 24, 2013, at 4:06 PM, "Guest, Simon"  
wrote:
> 
> Hi Greg,
> 
> Thanks for the explanation, and the link to that helpful Wiki page.
> And also that code update 4:71c35dbde130 which will help our tool
> test/development cycle.
> 
> I have a remaining question, though, about the recommended working
> practices for developing a toolshed tool.  I didn't find this
> described on the Wiki.  There is obviously a cycle of development to
> go through, making updates, installing to a test galaxy instance, etc.
> It seems to us that the only sensible way to handle this is within a
> local test toolshed, essentially using the repo in the test toolshed
> as a development repo (despite the warnings not use the toolshed as a
> source code repo on the Wiki!).  

This is certainly a good approach, although using a local tool shed as a 
component of the devlopment process when developing tools is probably useful 
only when your repository includes repository dependency definitions or tool 
dependency definitions.  In these cases, the tool shed encironment becomes 
useful for working out the details of the dependencies and making sure that 
everything ( all repository and tool dependencies ) installs correctly into 
your local Galaxy instance.

In cases where you are developing simpler tools ( e.g., Text Manipulation tools 
like filter and sort ) that are completely self contained ( they have no 
dependencies ), using a local tool shed during the development process is 
probably not necessary.



> During such an iterative process, we
> don't want to keep bumping the tool version.  

It may ot be necessary to do so - the only time you should be bumping the tool 
version ( which is a manual process of changing the version string in the tool 
config ) is when the tool behavior changes such that the same input dataset 
produces defferent resulting output datasets(s).

> Therefore it seems
> necessary to reset the repository meta data after every push, in order
> to install the just-updated-for-testing tool.  

If you are using mercurial ersion 2.2.3 or later in your shell environment, 
then pushing to your local tool shed from the command line should be resetting 
metadata back to the last installable changeset revsion.  If you are not seeing 
this behavior, make sure you are using that version or later - see 
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line


> Once the tool is
> working, the files can be uploaded into a clean repo on a production
> toolshed, so we don't keep all the intermediate development versions.


Yes, this is definitely the correct approach if you do find that using a local 
tool shed during the development process is beneficial.


> 
> Or is there a better way to do this?


I think you have things pretty well figured out.  Don't hesitate to continue to 
ask questions as they arise.


> 
> cheers,
> Simon
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Re: [galaxy-dev] Toolshed reset all repository metadata

[Guest, Simon]

At Thu, 24 Oct 2013 10:03:14 -0400,
Greg Von Kuster wrote:
> 
> Hello Simon,
> 
> On Oct 23, 2013, at 5:01 PM, Simon Guest  wrote:
> 
> > We've noticed a funny about resetting repository metadata from the
> > toolshed web interface.
> > 
> > My understanding is that this is used to get the toolshed back in sync
> > with the underlying mercurial repo, for example after pushing updates
> > from hg on the command line.
> 
> This is not quite correct.  When committing a new changeset to a repository 
> (either via hg push from the command line or by using any feature in the Tool 
> Shed's upload component), metadata is reset on the repository automatically, 
> but only back to the previous installable changeset revision if one exists.  
> So for those repositories that have multiple changeset revisions, not all of 
> the repository changelog is inspected with a new commit.
> 
> The "Reset all repository metadata" feature, however, does inspect the 
> complete repository changelog and resets metadata from revision 0 through the 
> repository tip.  In addition to being useful for the current repository 
> itself, it can also be useful for all other repositories that have a 
> dependency relationship to it.  See 
> http://wiki.galaxyproject.org/RepositoryRevisions#Resetting_metadata_on_your_repositories.
> 
> In general, it is not necessary to use this feature.

Hi Greg,

Thanks for the explanation, and the link to that helpful Wiki page.
And also that code update 4:71c35dbde130 which will help our tool
test/development cycle.

I have a remaining question, though, about the recommended working
practices for developing a toolshed tool.  I didn't find this
described on the Wiki.  There is obviously a cycle of development to
go through, making updates, installing to a test galaxy instance, etc.
It seems to us that the only sensible way to handle this is within a
local test toolshed, essentially using the repo in the test toolshed
as a development repo (despite the warnings not use the toolshed as a
source code repo on the Wiki!).  During such an iterative process, we
don't want to keep bumping the tool version.  Therefore it seems
necessary to reset the repository meta data after every push, in order
to install the just-updated-for-testing tool.  Once the tool is
working, the files can be uploaded into a clean repo on a production
toolshed, so we don't keep all the intermediate development versions.

Or is there a better way to do this?

cheers,
Simon
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Re: [galaxy-dev] Toolshed reset all repository metadata

[Greg Von Kuster]

Hello Simon,

On Oct 23, 2013, at 5:01 PM, Simon Guest  wrote:

> We've noticed a funny about resetting repository metadata from the
> toolshed web interface.
> 
> My understanding is that this is used to get the toolshed back in sync
> with the underlying mercurial repo, for example after pushing updates
> from hg on the command line.

This is not quite correct.  When committing a new changeset to a repository 
(either via hg push from the command line or by using any feature in the Tool 
Shed's upload component), metadata is reset on the repository automatically, 
but only back to the previous installable changeset revision if one exists.  So 
for those repositories that have multiple changeset revisions, not all of the 
repository changelog is inspected with a new commit.

The "Reset all repository metadata" feature, however, does inspect the complete 
repository changelog and resets metadata from revision 0 through the repository 
tip.  In addition to being useful for the current repository itself, it can 
also be useful for all other repositories that have a dependency relationship 
to it.  See 
http://wiki.galaxyproject.org/RepositoryRevisions#Resetting_metadata_on_your_repositories.

In general, it is not necessary to use this feature.


> 
> It seems that only the person who created the repository can reset
> metadata.  I granted authority to make changes to a colleague, which
> enables him to push updates, but he doesn't see the reset metadata
> entry in the menu.  This seems like a bug to me.  Or is it by design?

This was the original desing, but a more recent oversight as this feature has 
evolved.  This has been corrected in 4:71c35dbde130, which i committed to 
the next-stable branch and is now running on both the test and main Galaxy tol 
sheds.


> 
> Also, is there a reason why this function is necessary at all?


Yes, but it is not generally necessary for it to be used.  It used to be 
restricted to only a Tool Shed admin, but recently it was exposed to repository 
owners (and noew anyone tha thas write access) because it became very useful 
for developers like Bjoern Gruening to be able to reset metadata on 
repositories (especially in the test tool shed) as new repository and tools 
dependency relationship features were being introduced at the same time as 
repository types (TOOL_DEPENDENCY_DEFINITION) and he was helping to flesh out 
the support for the new features.


> Wouldn't it be better if the toolshed just noticed updates to the
> underlying mercurial repo, and reset its own metadata automatically?

It does, but hopefully my explanations above, as well as the details in the 
referenced tool shed wiki page will clarify this feature for you.


> 
> cheers,
> Simon
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Re: [galaxy-dev] Toolshed Collaboration Issues

[Björn Grüning]

Hi,

I added you successfully to:

http://testtoolshed.g2.bx.psu.edu/view/bgruening/precommit_test

please keep in mind that you need to remove the 'select one' button
before you click submit, that is not intuitive but a known bug.

Cheers,
Bjoern

> Perhaps it has something to do with a specific account?  The user
> 'nilesh' tried to add me to his rseqc repository
> (http://toolshed.g2.bx.psu.edu/view/nilesh/rseqc ) and got a Server
> Error.  I then created the rseqc_dev3 repository
> (http://testtoolshed.g2.bx.psu.edu/view/lparsons/rseqc_dev3 ) on the
> testtoolshed and tried to add him (nilesh) and got the error indicated
> below.  Any help in tracking this down would be appreciated.
> 
> Björn Grüning wrote: 
> > Hi Lance,
> > 
> > I worked for me the last time. I usually create a repository under the
> > IUC account and add me as contributor. No problem so far.
> > 
> > Cheers,
> > Bjoern
> > 
> > > I'm having some difficulty collaborating on a tool development in the 
> > > toolshed.  It seems to happen on the production toolshed as well as the 
> > > testtoolshed.  When I try to grant another user the ability to update a 
> > > repository (or when the other person tries to add me) we get the 
> > > following error:
> > > 
> > > URL: 
> > > http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py',
> > >  
> > > line 149 in __call__
> > >app_iter = self.application(environ, sr_checker)
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py',
> > >  
> > > line 106 in __call__
> > >environ, self.app)
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py',
> > >  
> > > line 543 in intercept_output
> > >app_iter = application(environ, replacement_start_response)
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
> > >  
> > > line 84 in __call__
> > >return self.application(environ, start_response)
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
> > >  
> > > line 633 in __call__
> > >return self.application(environ, start_response)
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py',
> > >  
> > > line 132 in __call__
> > >return self.handle_request( environ, start_response )
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py',
> > >  
> > > line 190 in handle_request
> > >body = method( trans, **kwargs )
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py',
> > >  
> > > line 98 in decorator
> > >return func( self, trans, *args, **kwargs )
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py',
> > >  
> > > line 2124 in manage_repository
> > >user = trans.sa_session.query( trans.model.User ).get( 
> > > trans.security.decode_id( user_id ) )
> > > File 
> > > '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py',
> > >  
> > > line 60 in decode_id
> > >return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( 
> > > "!" ) )
> > > File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode
> > >output = binascii.a2b_hex(input)
> > > TypeError: Non-hexadecimal digit found
> > > 
> > > Can anyone else successfully grant a user update permission to a 
> > > repository?  I've submitted an issue on Trello 
> > > (https://trello.com/c/XYkqW3Lr).
> > > 
> > > 
> > 
> > 
> > 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> 



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Re: [galaxy-dev] Toolshed Collaboration Issues

[Lance Parsons]

Perhaps it has something to do with a specific account?  The user 
'nilesh' tried to add me to his rseqc repository 
(http://toolshed.g2.bx.psu.edu/view/nilesh/rseqc ) and got a Server 
Error.  I then created the rseqc_dev3 repository 
(http://testtoolshed.g2.bx.psu.edu/view/lparsons/rseqc_dev3 )on the 
testtoolshed and tried to add him (nilesh) and got the error indicated 
below.  Any help in tracking this down would be appreciated.


Björn Grüning wrote:

Hi Lance,

I worked for me the last time. I usually create a repository under the
IUC account and add me as contributor. No problem so far.

Cheers,
Bjoern


I'm having some difficulty collaborating on a tool development in the
toolshed.  It seems to happen on the production toolshed as well as the
testtoolshed.  When I try to grant another user the ability to update a
repository (or when the other person tries to add me) we get the
following error:

URL:
http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py',
line 106 in __call__
environ, self.app)
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py',
line 543 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py',
line 98 in decorator
return func( self, trans, *args, **kwargs )
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py',
line 2124 in manage_repository
user = trans.sa_session.query( trans.model.User ).get(
trans.security.decode_id( user_id ) )
File
'/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py',
line 60 in decode_id
return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip(
"!" ) )
File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode
output = binascii.a2b_hex(input)
TypeError: Non-hexadecimal digit found

Can anyone else successfully grant a user update permission to a
repository?  I've submitted an issue on Trello
(https://trello.com/c/XYkqW3Lr).








--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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Re: [galaxy-dev] Toolshed Collaboration Issues

[Björn Grüning]

Hi Lance,

I worked for me the last time. I usually create a repository under the
IUC account and add me as contributor. No problem so far.

Cheers,
Bjoern

> I'm having some difficulty collaborating on a tool development in the 
> toolshed.  It seems to happen on the production toolshed as well as the 
> testtoolshed.  When I try to grant another user the ability to update a 
> repository (or when the other person tries to add me) we get the 
> following error:
> 
> URL: 
> http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded06bdcd9
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py',
>  
> line 149 in __call__
>app_iter = self.application(environ, sr_checker)
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py',
>  
> line 106 in __call__
>environ, self.app)
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py',
>  
> line 543 in intercept_output
>app_iter = application(environ, replacement_start_response)
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>  
> line 84 in __call__
>return self.application(environ, start_response)
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>  
> line 633 in __call__
>return self.application(environ, start_response)
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py',
>  
> line 132 in __call__
>return self.handle_request( environ, start_response )
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py',
>  
> line 190 in handle_request
>body = method( trans, **kwargs )
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py',
>  
> line 98 in decorator
>return func( self, trans, *args, **kwargs )
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py',
>  
> line 2124 in manage_repository
>user = trans.sa_session.query( trans.model.User ).get( 
> trans.security.decode_id( user_id ) )
> File 
> '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py',
>  
> line 60 in decode_id
>return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( 
> "!" ) )
> File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode
>output = binascii.a2b_hex(input)
> TypeError: Non-hexadecimal digit found
> 
> Can anyone else successfully grant a user update permission to a 
> repository?  I've submitted an issue on Trello 
> (https://trello.com/c/XYkqW3Lr).
> 
> 



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Re: [galaxy-dev] toolshed tool versions and tool panel

[Dave Bouvier]

Pieter,

Thank you for this report, I have reproduced this behavior in my local 
Galaxy instance. I did however notice that the tool version drop-down is 
still available on the tool's page, but multiple entries in the 
left-hand tool panel is not intended behavior. I've created a Trello 
card to track our progress on resolving that issue:


https://trello.com/c/SlNI79mR

   --Dave B.

On 09/13/2013 06:27 AM, Lukasse, Pieter wrote:

Hi Greg,

When updating the version number of a tool I noticed that, as expected,
both the old version and the new version of the tool become available in
the Galaxy environment. What I did not expect is that the new version
resulted in a new entry in the menu bar (see screenshot):

If I remember correctly, you showed in Oslo that the tool version
becomes a choice in the tool itself, something like the screenshot below:

Is this a setting somewhere or are we facing a bug?

Best regards,

Pieter.

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

+31-317480891; skype: pieter.lukasse.wur

http://www.pri.wur.nl 



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Re: [galaxy-dev] Toolshed repository update error

[Bjoern Gruening]

Hi Saskia,

you need to fix that wrapper. Its a merge conflict you need to resolve
by your own (indicated by << ==).

Cheers,
Bjoern

> I am working on putting a tool into the toolshed. I have a bash script
> wrapper. I uploaded the first version fine, but when I wanted to
> upload a revision, some unwanted characters are inserted around the
> revised function of my code (see bottom) ..the inserted "<< local"
> etc strings are causing my script to fail of course. How can I prevent
> this from happening? 
> 
> Saskia
> 
> 
> snippet of the code:
> 
> 
> if [[ ! -s $rfile ]] 
> then   
> dummycol=${addcols:2}
> outputcol=${dummycol//",B."/""}
> <<< local
> echo -e "${col_chr_name}\t${col_start_name}\t${col_end_name}\t
> ${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile
> cat $rfile
> ===
> numcommas=`echo "$addcols" | grep -o "," | wc -l`
> echo "numcolums: $numcommas"
> 
> awk 'BEGIN{FS="\t";OFS="\t"}{
> if(FNR==1)
> print $0,"'"$outputcol"'"; 
> else{
> printf $0
> for(i=0;i<="'"$numcommas"'"+1;i++)
> printf "\t"
> printf "\n"
> }
> }END{}' $ofile > tempofile
> 
> mv tempofile $ofile
> 
> return
> >>> other
> fi
> 
> 
> 
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Re: [galaxy-dev] ToolShed preview lacking controls

[Peter Cock]

On Mon, Jul 22, 2013 at 3:03 PM, Greg Von Kuster  wrote:
> Hi Peter,
>
> This is a known issue - there is a Trello card for it here:
>
> https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action
>
> Thanks,
>
> Greg Von Kuster

Thanks Greg - I've subscribed & voted for that issue :)

Peter
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Re: [galaxy-dev] ToolShed preview lacking controls

[Greg Von Kuster]

Hi Peter,

This is a known issue - there is a Trello card for it here:

https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action

Thanks,

Greg Von Kuster

On Jul 22, 2013, at 9:12 AM, Peter Cock  wrote:

> HI all,
> 
> I just had a query about some 'missing' functionality in one of my
> tools, which is handled by a parameter which doesn't get shown
> on the preview shown in the Tool Shed - perhaps because it is
> inside a conditional?
> 
> 
> 
> Both positive matches (ID on list) and negative
> matches (ID not on list), as two files
> Just positive matches (ID on list), as a single
> file
> Just negative matches (ID not on list), as a
> single file
> 
> 
> 
> 
> 
> 
> 
> Ideally the ToolShed preview would show the dropdown combo
> box allowing you to pick both files, positive only, or negative only:
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
> 
> Is this a known limitation? Is there a Trello card I should follow?
> 
> Thanks,
> 
> Peter
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Re: [galaxy-dev] ToolShed dependencies KeyError: 'invalid_repository_dependencies'

[Greg Von Kuster]

Hello Peter,

Thanks for reporting this - I have committed a fix in changeset 
10206:86efa5ac1fae, which is currently running on the test tool shed.

Greg Von Kuster

On Jul 8, 2013, at 11:35 AM, Peter Cock  wrote:

> Hi Greg,
> 
> Previously my workflows had hard coded dependencies on the main
> Tool Shed, which currently is a bit of a problem on the Test Tool Shed.
> 
> Therefore I'm update my Tool Shed workflows using a
> repository_dependencies.xml with implicit repository and revision fields
> (i.e. the latest revision within the current ToolShed).
> 
> It worked for one example but not the other - this turned out to be my
> own error, but the Tool Shed did not handle it gracefully. Perhaps
> this class of error could be caught instead? Thanks!
> 
> 
> 
> This worked, secreted_protein_workflow, Revision: 2:aecb871dfe4c
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
> 
> Input:
> 
> 
> 
>
>
>
>
> 
> 
> 
> 
> This failed, rxlr_venn_workflow, Revision: 3:65d174589251
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
> 
> On uploading the tar-ball I got this error in the browser:
> 
> 
> Internal Server Error
> Galaxy was unable to sucessfully complete your request
> 
> URL: 
> http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=20a9f7389ced5696
> Module galaxy.web.framework.middleware.error:149 in __call__
>>> app_iter = self.application(environ, sr_checker)
> Module paste.debug.prints:106 in __call__
>>> environ, self.app)
> Module paste.wsgilib:543 in intercept_output
>>> app_iter = application(environ, replacement_start_response)
> Module paste.recursive:84 in __call__
>>> return self.application(environ, start_response)
> Module paste.httpexceptions:633 in __call__
>>> return self.application(environ, start_response)
> Module galaxy.web.framework.base:132 in __call__
>>> return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:190 in handle_request
>>> body = method( trans, **kwargs )
> Module galaxy.web.framework:98 in decorator
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.tool_shed.controllers.upload:219 in upload
>>> invalid_repository_dependencies_message = 
>>> repository_dependency_util.generate_message_for_invalid_repository_dependencies(
>>>  metadata_dict )
> Module tool_shed.util.repository_dependency_util:252 in
> generate_message_for_invalid_repository_dependencies
>>> invalid_repository_dependencies = invalid_repository_dependencies_dict[ 
>>> 'invalid_repository_dependencies' ]
> KeyError: 'invalid_repository_dependencies'
> extra data
> 
> full traceback
> 
> text version
> 
> This may be an intermittent problem due to load or other unpredictable
> factors, reloading the page may address the problem.
> 
> 
> Input repository_dependencies.xml where for the tmhmm_and_signalp entry
> I am missing the 'n' in name:
> 
> 
> 
>
>
>
>
>
>
> 
> 
> Output repository_dependencies.xml with mangled tmhmm_and_signalp entry:
> 
> 
> 
>
> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
>
> name="seq_filter_by_id" owner="peterjc"
> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
>
> owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu"; />
> 
> 
> I corrected the ame/name error, and re-uploaded a fresh tar-ball which worked,
> Revision: 4:25e0ffd4f762
> 
> Peter
> ___
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Re: [galaxy-dev] Toolshed bug related to readme files

[Greg Von Kuster]

Hello Lance,

This issue should be corrected in change set 9994:f8cf776ff12f, which is 
currently running on both public tool sheds.  Thanks for reporting this!

Greg Von Kuster

On Jun 12, 2013, at 6:25 AM, Greg Von Kuster  wrote:

> Hi Lance,
> 
> Thanks for the information - I'll have a fix out shortly.
> 
> Greg Von Kuster
> 
> On Jun 11, 2013, at 10:12 PM, Lance Parsons  wrote:
> 
>> I'm running the latest stable.
>> 
>> The 500 error seems to be coming from the toolshed. Do you also get a 500 
>> error at the toolshed URL in my previous message? 
>> 
>> There is nothing other than standard info line from the request in my pasted 
>> log. I'm not able to get to the log right now, but I'll send it once I get a 
>> chance tomorrow.
>> 
>> 
>> -- 
>> Lance Parsons - Scientific Programmer
>> 134 Carl C. Icahn Laboratory
>> Lewis-Sigler Institute for Integrative Genomics
>> Princeton University
>> 
>> 
>> 
>>  Original message --------
>> From: Greg Von Kuster  
>> Date: 06/11/2013 10:00 PM (GMT-05:00) 
>> To: Lance Parsons  
>> Cc: galaxy-dev@lists.bx.psu.edu 
>> Subject: Re: [galaxy-dev] Toolshed bug related to readme files 
>> 
>> 
>> Hi Lance,
>> 
>> What version of Galaxy are you running?  Is the 500 error coming from your 
>> Galaxy server or the tool shed server?  Can you send the relevant 
>> information from your Galaxy paster log when attempting to reinstall?
>> 
>> Thanks,
>> 
>> Greg Von Kuster
>> 
>> 
>> On Jun 11, 2013, at 3:52 PM, Lance Parsons  wrote:
>> 
>>> I have run into an issue when trying to reinstall a tool that was 
>>> originally installed via migration scripts (toolshed version of picard).
>>> 
>>> When I attempt to reinstall (after successfully uninstalling) I get a 500 
>>> error.  After a bit of poking around, it seems that this URL generates the 
>>> 500 error:
>>> 
>>> http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
>>> 
>>> Looks like this changeset is relevant: 
>>> https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
>>> 
>>> 
>>> -- 
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>> 
>>> ___
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>>> http://galaxyproject.org/search/mailinglists/
>> 
>> 
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> 
> 
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Re: [galaxy-dev] Toolshed bug related to readme files

[Greg Von Kuster]

Hi Lance,

Thanks for the information - I'll have a fix out shortly.

Greg Von Kuster

On Jun 11, 2013, at 10:12 PM, Lance Parsons  wrote:

> I'm running the latest stable.
> 
> The 500 error seems to be coming from the toolshed. Do you also get a 500 
> error at the toolshed URL in my previous message? 
> 
> There is nothing other than standard info line from the request in my pasted 
> log. I'm not able to get to the log right now, but I'll send it once I get a 
> chance tomorrow.
> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> 
> 
>  Original message 
> From: Greg Von Kuster  
> Date: 06/11/2013 10:00 PM (GMT-05:00) 
> To: Lance Parsons  
> Cc: galaxy-dev@lists.bx.psu.edu 
> Subject: Re: [galaxy-dev] Toolshed bug related to readme files 
> 
> 
> Hi Lance,
> 
> What version of Galaxy are you running?  Is the 500 error coming from your 
> Galaxy server or the tool shed server?  Can you send the relevant information 
> from your Galaxy paster log when attempting to reinstall?
> 
> Thanks,
> 
> Greg Von Kuster
> 
> 
> On Jun 11, 2013, at 3:52 PM, Lance Parsons  wrote:
> 
> > I have run into an issue when trying to reinstall a tool that was 
> > originally installed via migration scripts (toolshed version of picard).
> > 
> > When I attempt to reinstall (after successfully uninstalling) I get a 500 
> > error.  After a bit of poking around, it seems that this URL generates the 
> > 500 error:
> > 
> > http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
> > 
> > Looks like this changeset is relevant: 
> > https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
> > 
> > 
> > -- 
> > Lance Parsons - Scientific Programmer
> > 134 Carl C. Icahn Laboratory
> > Lewis-Sigler Institute for Integrative Genomics
> > Princeton University
> > 
> > ___
> > 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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> 
> 
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Re: [galaxy-dev] Toolshed bug related to readme files

[Lance Parsons]

I'm running the latest stable.

The 500 error seems to be coming from the toolshed. Do you also get a 500 error 
at the toolshed URL in my previous message? 

There is nothing other than standard info line from the request in my pasted 
log. I'm not able to get to the log right now, but I'll send it once I get a 
chance tomorrow.


-- 
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

 Original message 
From: Greg Von Kuster  
Date: 06/11/2013  10:00 PM  (GMT-05:00) 
To: Lance Parsons  
Cc: galaxy-dev@lists.bx.psu.edu 
Subject: Re: [galaxy-dev] Toolshed bug related to readme files 
 
Hi Lance,

What version of Galaxy are you running?  Is the 500 error coming from your 
Galaxy server or the tool shed server?  Can you send the relevant information 
from your Galaxy paster log when attempting to reinstall?

Thanks,

Greg Von Kuster


On Jun 11, 2013, at 3:52 PM, Lance Parsons  wrote:

> I have run into an issue when trying to reinstall a tool that was originally 
> installed via migration scripts (toolshed version of picard).
> 
> When I attempt to reinstall (after successfully uninstalling) I get a 500 
> error.  After a bit of poking around, it seems that this URL generates the 
> 500 error:
> 
> http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
> 
> Looks like this changeset is relevant: 
> https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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> 
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> http://galaxyproject.org/search/mailinglists/


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Re: [galaxy-dev] Toolshed bug related to readme files

[Greg Von Kuster]

Hi Lance,

What version of Galaxy are you running?  Is the 500 error coming from your 
Galaxy server or the tool shed server?  Can you send the relevant information 
from your Galaxy paster log when attempting to reinstall?

Thanks,

Greg Von Kuster


On Jun 11, 2013, at 3:52 PM, Lance Parsons  wrote:

> I have run into an issue when trying to reinstall a tool that was originally 
> installed via migration scripts (toolshed version of picard).
> 
> When I attempt to reinstall (after successfully uninstalling) I get a 500 
> error.  After a bit of poking around, it seems that this URL generates the 
> 500 error:
> 
> http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picard&owner=devteam&changeset_revision=e0232cbac965
> 
> Looks like this changeset is relevant: 
> https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696
> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
> 
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Re: [galaxy-dev] Toolshed tool doesn't exist error after installation from toolshed

[Greg Von Kuster]

Hi Simon,

I just installe dour fasta_stats repository form the test tool shed and 
successfully executed your fast statistics tool, so I am not able to reproduce 
this behavior.  There must be a configuration problem in your local Galaxy 
instance that is resulting in this behavior, but I cannot tell you what it is.  
The problem seems to be that your fasta statistics tool is not properly loaded 
into your Galaxy tool box, so your paster log should show an exception when 
attempting to load the tool after the repository is installed.  Here's what my 
paster log shows, what does yours show?

Thanks,

Greg Von Kuster

127.0.0.1 - - [11/Jun/2013:08:52:49 -0400] "GET 
/admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F
 HTTP/1.1" 302 - "http://localhost:8763/admin_toolshed/browse_tool_sheds"; 
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101 
Firefox/21.0"
127.0.0.1 - - [11/Jun/2013:08:53:15 -0400] "GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=ea3d74feddb3e781&changeset_revisions=3eca3cb79e74
 HTTP/1.1" 200 - 
"http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ea3d74feddb3e781&changeset_revision=3eca3cb79e74";
 "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101 
Firefox/21.0"
tool_shed.util.tool_util DEBUG 2013-06-11 08:53:20,794 Loading new tool panel 
section: fasta
tool_shed.util.shed_util_common DEBUG 2013-06-11 08:53:20,794 Adding new row 
(or updating an existing row) for repository 'fasta_stats' in the 
tool_shed_repository table.
tool_shed.util.tool_util DEBUG 2013-06-11 08:53:20,835 Appending to tool panel 
section: fasta
127.0.0.1 - - [11/Jun/2013:08:53:20 -0400] "POST 
/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=7f7b0676b166777988637e98c4b4cf254cac31b0%3A7b2266617374615f7374617473223a205b2250726f647563652062617369632073746174697374696373206f6e20612066617374612f6d756c746966617374612066696c65222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f73696d6f6e2d676c61646d616e2f66617374615f7374617473222c2022336563613363623739653734222c202231222c202273696d6f6e2d676c61646d616e222c207b7d2c207b7d5d7d&includes_tools=True&tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=False
 HTTP/1.1" 200 - 
"http://localhost:8763/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=ea3d74feddb3e781&changeset_revisions=3eca3cb79e74";
 "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101 
Firefox/21.0"
/Users/gvk/workspace/galaxy-central/lib/tool_shed/util/xml_util.py:90: 
FutureWarning: The behavior of this method will change in future versions.  Use 
specific 'len(elem)' or 'elem is not None' test instead.
  if elem:
galaxy.tools DEBUG 2013-06-11 08:53:21,609 Loaded tool id: 
testtoolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0, 
version: 1.0.0 into tool panel.



On Jun 11, 2013, at 12:37 AM, Simon Gladman  wrote:

> Hi all,
> 
> Looked for this in the list but couldn't find it. Admittedly I was using 
> gmail to search the list so I may have missed it - apologies if so.
> 
> I have put a very simple tool into a local toolshed (latest version of 
> toolshed) which just consists of an xml wrapper and a perl script in the 
> repository. (attached) I want to test it prior to putting it in the main 
> toolshed..
> 
> When I install the tool into my galaxy (latest-stable version) it installs ok.
> 
> I then go to run the tool and it loads the interface quite happily but upon 
> execute it says tool doesn't exist.
> 
> I think its looking in the wrong folder on the server for the tool.
> 
> In the main galaxy window: 
> 
> Tool 
> 'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' 
> does not exist, kwd={'tool_state': 
> u'80025569356339643261396332633035356535356161303366316533393935313439613834366130616239363a3762323235663566373036313637363535663566323233613230333032633230323236343631373436313733363537343232336132303232333233323232376471002e',
>  'runtool_btn': u'Execute', 'refresh': u'refresh', 'dataset': u'22'}
> 
> In the server log:
> 
> galaxy.webapps.galaxy.controllers.tool_runner ERROR 2013-06-11 14:23:14,434 
> index called with tool id 
> 'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0' 
> but no such tool exists
> 128.250.103.244 - - [11/Jun/2013:14:23:14 +1100] "POST /tool_runner/index 
> HTTP/1.1" 200 - 
> "https://galaxy-vbc-test.monash.edu/tool_runner?tool_id=galaxy-dev.genome.edu.au%3A9009/repos/slugger/fasta_stats/fasta-stats/1.0.0";
>  "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
> Chrome/27.0.1453.110 Safari/537.36"
> 
> The tool is installed in (via the toolshed install process):
> 
> shed_tools/galaxy-dev.genome.edu.au/repos/slugger/fasta_stats/9

Re: [galaxy-dev] toolshed down?

[Greg Von Kuster]

Both tool shed's should now be accessible.  Sorry for the downtime.


On May 2, 2013, at 6:26 AM, Greg Von Kuster wrote:

> Hello Geert,
> 
> Thanks for reporting this - it looks like our server or network is down.  
> We'll get this resolved as soon as possible and let you know when it is 
> available.
> 
> Greg Von Kuster
> 
> On May 2, 2013, at 6:16 AM, Geert Vandeweyer wrote:
> 
>> hi,
>> 
>> I'm getting the following error when trying to reach the main/test 
>> toolsheds. Are they down?
>> 
>> 
>> 
>> This webpage is not available
>> Chromium's connection attempt to toolshed.g2.bx.psu.edu was rejected. The 
>> website may be down, or your network may not be properly configured.
>> 
>> 
>> also from within galaxy, I can't reach it, nor can the galaxy-process itself:
>> 
>> galaxy.model.migrate.check INFO 2013-05-02 12:12:45,219 At database version 
>> 114
>> tool_shed.galaxy_install.migrate.check DEBUG 2013-05-02 12:12:45,390 
>> pysqlite>=2 egg successfully loaded for sqlite dialect
>> The URL
>> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_wrappers&owner=devteam&changeset_revision=0c7e4eadfb3c&from_install_manager=True
>> raised the exception:
>> 
>> 
>> The URL
>> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_color_wrappers&owner=devteam&changeset_revision=fd0914e451c5&from_install_manager=True
>> raised the exception:
>> 
>> 
>> The URL
>> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz&owner=devteam&changeset_revision=0801f8207d30&from_install_manager=True
>> raised the exception:
>> 
>> 
>> The URL
>> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_paired_reads&owner=devteam&changeset_revision=96825cee5c25&from_install_manager=True
>> raised the exception:
>> 
>> 
>> Traceback (most recent call last):
>> File 
>> "/galaxy/galaxy-beta/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", 
>> line 37, in app_factory
>>   app = UniverseApplication( global_conf = global_conf, **kwargs )
>> File "/galaxy/galaxy-beta/galaxy-dist/lib/galaxy/app.py", line 54, in 
>> __init__
>>   verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( 
>> '__file__', None ), self.config.database_engine_options )
>> File 
>> "/galaxy/galaxy-beta/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py",
>>  line 56, in verify_tools
>>   tool_shed_accessible, missing_tool_configs_dict = 
>> common_util.check_for_missing_tools( app, tool_panel_configs, 
>> latest_tool_migration_script_number )
>> File "/galaxy/galaxy-beta/galaxy-dist/lib/tool_shed/util/common_util.py", 
>> line 66, in check_for_missing_tools
>>   return tool_shed_accessible, missing_tool_configs_dict
>> UnboundLocalError: local variable 'missing_tool_configs_dict' referenced 
>> before assignment
>> 
>> 
>> -- 
>> 
>> Geert Vandeweyer, Ph.D.
>> Department of Medical Genetics
>> University of Antwerp
>> Prins Boudewijnlaan 43
>> 2650 Edegem
>> Belgium
>> Tel: +32 (0)3 275 97 56
>> E-mail: geert.vandewe...@ua.ac.be
>> http://ua.ac.be/cognitivegenetics
>> http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>> 
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>> 
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>> http://galaxyproject.org/search/mailinglists/
> 


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Re: [galaxy-dev] toolshed down?

[Greg Von Kuster]

Hello Geert,

Thanks for reporting this - it looks like our server or network is down.  We'll 
get this resolved as soon as possible and let you know when it is available.

Greg Von Kuster

On May 2, 2013, at 6:16 AM, Geert Vandeweyer wrote:

> hi,
> 
> I'm getting the following error when trying to reach the main/test toolsheds. 
> Are they down?
> 
> 
> 
> This webpage is not available
> Chromium's connection attempt to toolshed.g2.bx.psu.edu was rejected. The 
> website may be down, or your network may not be properly configured.
> 
> 
> also from within galaxy, I can't reach it, nor can the galaxy-process itself:
> 
> galaxy.model.migrate.check INFO 2013-05-02 12:12:45,219 At database version 
> 114
> tool_shed.galaxy_install.migrate.check DEBUG 2013-05-02 12:12:45,390 
> pysqlite>=2 egg successfully loaded for sqlite dialect
> The URL
> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_wrappers&owner=devteam&changeset_revision=0c7e4eadfb3c&from_install_manager=True
> raised the exception:
> 
> 
> The URL
> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_color_wrappers&owner=devteam&changeset_revision=fd0914e451c5&from_install_manager=True
> raised the exception:
> 
> 
> The URL
> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz&owner=devteam&changeset_revision=0801f8207d30&from_install_manager=True
> raised the exception:
> 
> 
> The URL
> http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_paired_reads&owner=devteam&changeset_revision=96825cee5c25&from_install_manager=True
> raised the exception:
> 
> 
> Traceback (most recent call last):
>  File 
> "/galaxy/galaxy-beta/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
> 37, in app_factory
>app = UniverseApplication( global_conf = global_conf, **kwargs )
>  File "/galaxy/galaxy-beta/galaxy-dist/lib/galaxy/app.py", line 54, in 
> __init__
>verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( 
> '__file__', None ), self.config.database_engine_options )
>  File 
> "/galaxy/galaxy-beta/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py",
>  line 56, in verify_tools
>tool_shed_accessible, missing_tool_configs_dict = 
> common_util.check_for_missing_tools( app, tool_panel_configs, 
> latest_tool_migration_script_number )
>  File "/galaxy/galaxy-beta/galaxy-dist/lib/tool_shed/util/common_util.py", 
> line 66, in check_for_missing_tools
>return tool_shed_accessible, missing_tool_configs_dict
> UnboundLocalError: local variable 'missing_tool_configs_dict' referenced 
> before assignment
> 
> 
> -- 
> 
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
> 
> ___
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Re: [galaxy-dev] toolshed gives internal server error

[Hollander, Mattias de]

Thanks for fixing!

On 05/01/2013 04:29 PM, Dave Bouvier wrote:
> Mattias,
>
> Thank you for reporting this error, the issue has been resolved, and 
> downloading zipped files from the main tool shed is working.
>
>--Dave B.
>
> On 5/1/13 08:55:50.000, Greg Von Kuster wrote:
>> Hello Mattias,
>>
>> I've created the following Trello card for this and we'll get it 
>> fixed asap.  Thanks for letting us know.
>>
>> https://trello.com/card/toolshed-unable-to-download-repositories-as-zipped-archives/506338ce32ae458f6d15e4b3/824
>>  
>>
>>
>> Greg Von Kuster
>>
>>
>> On Apr 29, 2013, at 3:35 AM, Hollander, Mattias de wrote:
>>
>>> Hi Greg,
>>>
>>> I am trying to download the wrappers for repeatmasker from the general
>>> toolshed (http://toolshed.g2.bx.psu.edu/), but I retrieve an 'Internal
>>> Server Error' when I want to download the tar.gz (or any other zipped
>>> file) via the Repository Actions menu.
>>>
>>> Can you have a look at it?
>>>
>>> Thanks!
>>>
>>> Mattias
>>
>>
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>>

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Re: [galaxy-dev] toolshed gives internal server error

[Dave Bouvier]

Mattias,

Thank you for reporting this error, the issue has been resolved, and 
downloading zipped files from the main tool shed is working.


   --Dave B.

On 5/1/13 08:55:50.000, Greg Von Kuster wrote:

Hello Mattias,

I've created the following Trello card for this and we'll get it fixed asap.  
Thanks for letting us know.

https://trello.com/card/toolshed-unable-to-download-repositories-as-zipped-archives/506338ce32ae458f6d15e4b3/824

Greg Von Kuster


On Apr 29, 2013, at 3:35 AM, Hollander, Mattias de wrote:


Hi Greg,

I am trying to download the wrappers for repeatmasker from the general
toolshed (http://toolshed.g2.bx.psu.edu/), but I retrieve an 'Internal
Server Error' when I want to download the tar.gz (or any other zipped
file) via the Repository Actions menu.

Can you have a look at it?

Thanks!

Mattias



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Re: [galaxy-dev] toolshed gives internal server error

[Greg Von Kuster]

Hello Mattias,

I've created the following Trello card for this and we'll get it fixed asap.  
Thanks for letting us know.

https://trello.com/card/toolshed-unable-to-download-repositories-as-zipped-archives/506338ce32ae458f6d15e4b3/824

Greg Von Kuster


On Apr 29, 2013, at 3:35 AM, Hollander, Mattias de wrote:

> Hi Greg,
> 
> I am trying to download the wrappers for repeatmasker from the general 
> toolshed (http://toolshed.g2.bx.psu.edu/), but I retrieve an 'Internal 
> Server Error' when I want to download the tar.gz (or any other zipped 
> file) via the Repository Actions menu.
> 
> Can you have a look at it?
> 
> Thanks!
> 
> Mattias


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Re: [galaxy-dev] ToolShed test complaining core bundled test file is missing

[Peter Cock]

On Tue, Apr 23, 2013 at 4:01 PM, Dave Bouvier  wrote:
> Peter,
>
> Our approach has always been to treat each tool shed repository as a
> self-contained entity. This means that all required components are contained
> in the repository or definitions for obtaining them from remote repositories
> are contained in the repository.
>
> You'll notice that several tools that have been migrated to the tool shed
> from the distribution have 1.bed in their test-data directory. Our reasoning
> for that approach is that in the unlikely event that the distribution's
> version of 1.bed is changed, the repository version will still be valid for
> that repository's tool functional tests. Additionally, Ssuis.fasta may
> eventually be migrated out of the distribution, in which case any repository
> installed from the tool shed that depends on Ssuis.fasta will fail
> functional tests.
>
> However, I see your point about the file size, 1.9MB is a bit substantial
> for a test file. Is it possible to rewrite the test to use a smaller file?
>
>--Dave B.

Hmm. If that is the policy then I'll probably fall over some other examples
like this later on. I think in the short term I'll just bundle Ssuis.fasta with
this tool.

In this specific case, I noticed that Ssuis.fasta was included already,
and so it made a nice medium sized test case which would exercise
the code quite well. The alternative is to hand construct multiple
smaller test cases to try and cover corner cases deliberately - much
more work but perhaps a better route in the long term.

Thanks for quickly clarifying this,

Peter
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Re: [galaxy-dev] ToolShed test failure, "blastxml" ItemNotFoundError

[Peter Cock]

On Tue, Apr 23, 2013 at 3:32 PM, Dave Bouvier  wrote:
> Peter,
>
> You are correct, that is related to the issue described in the following
> trello card:
>
> https://trello.com/c/KdGX3hkh
>
> We are looking into a fix for that behavior, and I'll keep you posted.
>
>--Dave B.

Thanks - I've subscribed to that issue now.

Peter
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Re: [galaxy-dev] ToolShed test complaining core bundled test file is missing

[Dave Bouvier]

Peter,

Our approach has always been to treat each tool shed repository as a 
self-contained entity. This means that all required components are 
contained in the repository or definitions for obtaining them from 
remote repositories are contained in the repository.


You'll notice that several tools that have been migrated to the tool 
shed from the distribution have 1.bed in their test-data directory. Our 
reasoning for that approach is that in the unlikely event that the 
distribution's version of 1.bed is changed, the repository version will 
still be valid for that repository's tool functional tests. 
Additionally, Ssuis.fasta may eventually be migrated out of the 
distribution, in which case any repository installed from the tool shed 
that depends on Ssuis.fasta will fail functional tests.


However, I see your point about the file size, 1.9MB is a bit 
substantial for a test file. Is it possible to rewrite the test to use a 
smaller file?


   --Dave B.

On 4/23/13 10:25:38.000, Peter Cock wrote:

Hi Greg/Dave,

I've noticed an oddity with another unit test failure on the main Tool Shed,

http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
Revision: 1:922d69bd5258
Tool id: get_orfs_or_cdss version: 0.0.2
Reason test is invalid  One or more test files are missing for tool
get_orfs_or_cdss: Ssuis.fasta

The tool tests should be failing as they are omitting some test files, which
I'd not included in the uploaded tar ball (I'll fix this shortly):

test-data/get_orf_input.fasta
test-data/get_orf_input.Suis_ORF.nuc.fasta
test-data/get_orf_input.Suis_ORF.prot.fasta
test-data/get_orf_input.t11_nuc_out.fasta
test-data/get_orf_input.t11_open_nuc_out.fasta
test-data/get_orf_input.t11_open_prot_out.fasta
test-data/get_orf_input.t11_prot_out.fasta
test-data/get_orf_input.t1_nuc_out.fasta
test-data/get_orf_input.t1_prot_out.fasta

However, I believe the ToolShed warning is misleading as test-data/Ssuis.fasta
is already present as part of the Galaxy core install. This is why I
have used it
(and other bundled files like it) to minimise the download size of the
tool itself.

Thanks,

Peter
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Re: [galaxy-dev] ToolShed test failure, "blastxml" ItemNotFoundError

[Dave Bouvier]

Peter,

You are correct, that is related to the issue described in the following 
trello card:


https://trello.com/c/KdGX3hkh

We are looking into a fix for that behavior, and I'll keep you posted.

   --Dave B.

On 4/23/13 10:11:59.000, Peter Cock wrote:

Hi all,

I'm seeing a unit test failure on the Tool Shed which I think is in
some way related to the blast_datatypes dependency not
refreshing the list of available file formats:

http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr

Revision: 7:a7add03a44fd - blastxml_to_top_descr v0.0.6

Tool shed version: 9471:ae53deed05b6
Galaxy version: 9505:1e3d92ec22b2

Traceback (most recent call last):
   File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 171, in test_tool
 self.do_it( td, shed_tool_id=shed_tool_id )
   File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py",
line 43, in do_it
 shed_tool_id=shed_tool_id )
   File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 193, in upload_file
 self.refresh_form( "file_type", ftype ) #Refresh, to support composite 
files
   File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py",
line 1276, in refresh_form
 tc.fv( f.name, control.name, value )
   File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/commands.py",
line 450, in formvalue
 set_form_control_value(control, value)
   File 
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/utils.py",
line 190, in set_form_control_value
 raise ClientForm.ItemNotFoundError('cannot find value/label "%s"
in list control' % (val,))
ItemNotFoundError: cannot find value/label "blastxml" in list control

This bug reminds me of something recently discussed on the
list, but I can't find the thread (perhaps it was another file format).
So there may already be a Trello issue open for this.

Thanks,

Peter
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Re: [galaxy-dev] ToolShed functional tests bug

[Dave Bouvier]

Peter,

Again, thank you for reporting this issue, I've committed a fix in 
9470:d056556a1e63 and re-run the testing framework, and the functional 
test results page now shows the data for the tmhmm_and_signalp 
repository only.


   --Dave B.

On 4/16/13 16:47:25.000, Greg Von Kuster wrote:

Hello Peter,

Thanks for reporting this - I've created the following Trello card for this 
issue.  We'll get this fixed asap.

https://trello.com/card/toolshed-automated-functional-test-bug/506338ce32ae458f6d15e4b3/793

Greg Von Kuster


On Apr 15, 2013, at 11:21 AM, Peter Cock wrote:


On Thu, Apr 4, 2013 at 9:47 PM, Peter Cock  wrote:

Hi all,

I've been looking at the new functional test results now being
shown on the tool shed, and found a bug/glitch:

1. Goto http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
2. Click on top right menu "Repository Actions", "View functional test
results" menu item
3. Notice two failed tests for htseq_count (which is not in this repo)

This was for 12:6753a9261390 of this repo.

Peter


This bug is also happening on the Test Tool Shed, e.g.
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

Peter
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Re: [galaxy-dev] ToolShed functional tests bug

[Greg Von Kuster]

Hello Peter,

Thanks for reporting this - I've created the following Trello card for this 
issue.  We'll get this fixed asap.

https://trello.com/card/toolshed-automated-functional-test-bug/506338ce32ae458f6d15e4b3/793

Greg Von Kuster


On Apr 15, 2013, at 11:21 AM, Peter Cock wrote:

> On Thu, Apr 4, 2013 at 9:47 PM, Peter Cock  wrote:
>> Hi all,
>> 
>> I've been looking at the new functional test results now being
>> shown on the tool shed, and found a bug/glitch:
>> 
>> 1. Goto http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
>> 2. Click on top right menu "Repository Actions", "View functional test
>> results" menu item
>> 3. Notice two failed tests for htseq_count (which is not in this repo)
>> 
>> This was for 12:6753a9261390 of this repo.
>> 
>> Peter
> 
> This bug is also happening on the Test Tool Shed, e.g.
> http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> 
> Peter
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Re: [galaxy-dev] Toolshed errors

[Greg Von Kuster]

Hello Björn,

On Apr 6, 2013, at 9:06 AM, Björn Grüning wrote:

> Hi Greg and Dave,
> 
> good to know that it is at least installing :)
> I also tried without apache, fresh checkout and get the same timeouts.
> Maybe my computer is just so slow that its triggers the timeout. Also my
> Memory is very limited and nearly swapped during compilation.
> 
> But with the new API I'm able to install all of them just fine. Is that
> explainable?
> During my experiments I found that im not able to install the tools if a
> new-panel-section is supplied:
> 
> galaxy.web.framework ERROR 2013-04-06 14:29:05,411 Uncaught exception in
> exposed API method:
> 
> Traceback (most recent call last):
>  File
> "/home/bag/projects/galaxy/galaxy-central/lib/galaxy/web/framework/__init__.py",
>  line 196, in decorator
>rval = func( self, trans, *args, **kwargs)
>  File
> "/home/bag/projects/galaxy/galaxy-central/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py",
>  line 254, in install_repository_revision
>reinstalling=False )
>  File
> "/home/bag/projects/galaxy/galaxy-central/lib/tool_shed/galaxy_install/repository_util.py",
>  line 358, in install_tool_shed_repository
>if tool_panel_section_key:
>  File "/usr/lib/python2.7/UserDict.py", line 23, in __getitem__
>raise KeyError(key)
> KeyError: 'section_chemicaltoolbox'


This issue should be fixed in revision 3a07307 - thanks for reporting this!


> 
> Without that option it works. I tried to understand the code-path but
> found no section where a new entry is created under the toolbox. What I
> found is that: tool_panel_section_keys in repository_dependecy_util.py
> line 235 is updated every time and you will end up with several
> identical instances of 'section_chemicaltoolbox'. Hope that helps a
> little bit.

I'm not able to reproduce this (assuming it is not related to the issue I fixed 
above).  Is this issue now resolved for your?

> 
> Also please see a pull-request for a small typo:
> https://bitbucket.org/galaxy/galaxy-central/pull-request/150/change-error-message/diff


This pull request has been accepted  - thanks for the fixes!


> 
> Thanks for your work!
> Bjoern
> 
> 
> 
> 
>> Hello Björn,
>> 
>> Dave Bouvier (cc'd on this) spent some time yesterday inspecting the logs 
>> for out test tool shed and found no timeouts in either our paster log or our 
>> nginx log.  Dave was also successful in installing your repository and 
>> dependencies.  If I remember correctly, this timeout issue may be 
>> intermittent, but again, Dave found no logged timeout events at our end.  If 
>> you uncover any additional information, please let us know, and we'll 
>> continue to keep an eye on this.
>> 
>> Thanks very much,
>> 
>> Greg Von Kuster
>> 
>> 
>> On Apr 4, 2013, at 5:32 AM, Björn Grüning wrote:
>> 
>>> Hi Greg,
>>> 
>>> sorry forgot to attach the new traceback. Its now attached.
>>> If the grepping with the IP address did not work, maybe you can grep for
>>> the chemicaltoolbox/chemfp/openbabel/osra repositories. Im probably the
>>> only one working with it.
>>> 
>>> Have a nice day!
>>> Bjoern
>>> 
 Hello Björn,
 
 Thanks very much for your message!  Please see my inline comments.
 
 
 On Apr 2, 2013, at 4:33 PM, Björn Grüning wrote:
 
> I have tested a few things regarding to the toolshed and prepared a
> complex module-dependency-beast, with meta-package and
> orhphan-tool-dependencies and so on. A few problems I encountered are
> summarized below. You can try it by yourself, if you install the
> chemicaltoolbox package from the testtoolshed.
> 
> - three crashes with traceback attached, during tool-installation
> 
> - one 'name' not defined error, with attached patch
 
 
 Thanks very much for finding this issue and for the patch.  We've applied 
 it in changeset 9252:da2d6ee29f30 in our stable branch, so it is running 
 on both public Galaxy tool sheds.
 
 
> 
> - For me the the installation of tools with really complex and long
> compiling steps are stalled in 'Installing' forever. Try to install the
> osra package (it often hangs, but not every time). 
> Its not possible to uninstall/reinstall these dependencies
> without touching the database. And the error says, tool is already
> installed. Would be nice if the admin is able to reset that repository
> easily, even if it is limbo ... (is there a timeout somewhere?)
> Error: paste.httpserver.ThreadPool WARNING 2013-04-02 22:02:41,256 Thread 
> 140246687659776 hung (working on task for 1964 seconds)
> (The SystemExit: traceback attached)
 
 I've create the following Trello card for this issue:
 
 https://trello.com/card/toolshed-enable-galaxy-admin-to-reset-tool-dependencies-when-timeout-occurs/506338ce32ae458f6d15e4b3/761
 
 There are 4 places where this timeout may be occurring: Galaxy tool shed 
 server, Galaxy tool shed nginx, a p

Re: [galaxy-dev] ToolShed functional tests bug

[Peter Cock]

On Thu, Apr 4, 2013 at 9:47 PM, Peter Cock  wrote:
> Hi all,
>
> I've been looking at the new functional test results now being
> shown on the tool shed, and found a bug/glitch:
>
> 1. Goto http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> 2. Click on top right menu "Repository Actions", "View functional test
> results" menu item
> 3. Notice two failed tests for htseq_count (which is not in this repo)
>
> This was for 12:6753a9261390 of this repo.
>
> Peter

This bug is also happening on the Test Tool Shed, e.g.
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

Peter
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Re: [galaxy-dev] Toolshed errors

[Greg Von Kuster]

Hello Björn,

Thanks very much for your message!  Please see my inline comments.


On Apr 2, 2013, at 4:33 PM, Björn Grüning wrote:

> I have tested a few things regarding to the toolshed and prepared a
> complex module-dependency-beast, with meta-package and
> orhphan-tool-dependencies and so on. A few problems I encountered are
> summarized below. You can try it by yourself, if you install the
> chemicaltoolbox package from the testtoolshed.
> 
> - three crashes with traceback attached, during tool-installation
> 
> - one 'name' not defined error, with attached patch


Thanks very much for finding this issue and for the patch.  We've applied it in 
changeset 9252:da2d6ee29f30 in our stable branch, so it is running on both 
public Galaxy tool sheds.


> 
> - For me the the installation of tools with really complex and long
> compiling steps are stalled in 'Installing' forever. Try to install the
> osra package (it often hangs, but not every time). 
> Its not possible to uninstall/reinstall these dependencies
> without touching the database. And the error says, tool is already
> installed. Would be nice if the admin is able to reset that repository
> easily, even if it is limbo ... (is there a timeout somewhere?)
> Error: paste.httpserver.ThreadPool WARNING 2013-04-02 22:02:41,256 Thread 
> 140246687659776 hung (working on task for 1964 seconds)
> (The SystemExit: traceback attached)

I've create the following Trello card for this issue:

https://trello.com/card/toolshed-enable-galaxy-admin-to-reset-tool-dependencies-when-timeout-occurs/506338ce32ae458f6d15e4b3/761

There are 4 places where this timeout may be occurring: Galaxy tool shed 
server, Galaxy tool shed nginx, a proxy server at your end, or your local 
Galaxy server.  There is not enough information in your attached traceback log 
to determine where the timeout is occurring.  Can you provide me your Galaxy 
server's IP address so I can look in logs at our end?


> 
> - It would be great if the tool-developer or the admin has more control
> over the location of the tools in the toolbar. Installing meta package
> leaves you with only one choice, regardless how many tools are bundled. 


Support for this will be available in the next Galaxy release.  There are 
Trello cards for this here:

https://trello.com/card/toolshed-enhance-the-current-galaxy-api-for-installing-repositories-from-the-tool-shed/506338ce32ae458f6d15e4b3/734
https://trello.com/card/toolshed-add-features-that-leverage-the-galaxy-api-for-installing-repositories-from-the-tool-shed/506338ce32ae458f6d15e4b3/735


> 
> - Installing dependencies will leave me with empty folders under
> galaxy-root with the name of the dependency. My guess is, 
> that if I manually download a file/folder with wget, the folder is not 
> purged, but the content is.


Our intent is that installing repositories from the tool shed is completely 
automated with no manual intervention required.  Tool dependency definitions 
should not use utilities like wget to download dependencies because these 
utilities may not be available in the environments (e.g. vanilla mac os) into 
which the repositories are being installed.  I'll enhance the tool dependency 
tag sets as necessary to accommodate additional download and install 
requirements.  Can you let me know if the current download_by_url needs 
enhancements?


> 
> - Often after upgrading the tool_dependencies.xml file, I was not able
> to 'get updates' from the toolshed. The version was up-to-data, but it
> wasn't. Deinstalling and Installing fixed it. But I think its ab bug,
> isn't it?

This very well may be a bug.  Can you please provide additional details so that 
I can reproduce this behavior?  I'll get a fix asap.


> 
> - Is there a way, to just download a python file, not zipped and add it to 
> PYTHONPATH?
> If I download it with  I have problems to copy 
> that file with move.
> I would like to download it with wget, but one download by URL is required. 
> My current solution is, 
> to include a dummy download_by_url and than fetch with wget, or download a 
> archive version.

I've created the following Trello card for this issue:

https://trello.com/card/toolshed-enhance-the-download-by-url-process-for-installing-tool-dependencies/506338ce32ae458f6d15e4b3/760


> 
> - Is it correct that a repository referenced only in
> tool_dependencies.xml is not enough to install? numpy was only
> referenced as tool_dependency and I got the error that the tool (with
> owner and revision) was not found. After adding to repository_dependency
> it was ok.

Can you provide more details about your question above (e.g., the 
tool_dependencies.xml fie would help).  I want to make sure i understand the 
issue.  

Thanks very much Björn,

Greg Von Kuster




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Re: [galaxy-dev] Toolshed - Installation of static files

[Greg Von Kuster]

Hello Lance,

I've committed a fix for this issue into the next-stable branch on the 
galaxy-central repository in change set revision 9212:92c8a55a6679, so the fix 
will be included in the upcoming Galaxy release.  This fix is currently running 
on both the test and main Galaxy tool sheds as well.

You'll need to change your tool config file to use a new reserved word as 
follows:

.. image:: $PATH_TO_IMAGES/count_modes.png

This reserved word will route correctly in the tool shed when you display the 
tool inside of it's containing repository, and it will also route correctly 
when the tool is loaded from it's repository after it has been installed into 
Galaxy.  

All future tool configs that display images in the tool's help section will 
need to use this approach for tools included in repositories in the tool shed.

Thanks very much for reporting this issue, and please let me know if you run 
into any issues.

Greg Von Kuster


On Mar 22, 2013, at 1:50 PM, Lance Parsons wrote:

> Thanks for the quick response Greg.  I tried this and uploaded an update to 
> the testtoolshed and installed that in a test instance of Galaxy.  
> Unfortunately, it didn't seem to resolve the issue.  Galaxy still renders the 
> html with the image source pointing to the same location (e.g. 
> http://127.0.0.1:8080/static/images/count_modes.png).  This doesn't resolve.
> 
> You can try installing the htseq_count package from the testtoolshed to see 
> the issue for yourself. 
> 
> Lance
> 
> Greg Von Kuster wrote:
>> 
>> Hi Lance,
>> 
>> I answered this in your previous email - here's the answer:
>> 
>> To make this work in the tool shed, make the static directory that contains 
>> the image file a relative path in the tool config.  For example, your 
>> repository has the following structure:
>> 
>> htseq_count
>> htseq-count.xml
>> sam_fa_indices.loc.sample
>> static/
>>  images/
>>  count_modes.png
>> test-data/
>>  tool_data_table_conf.xml.sample
>>  tool_dependencies.xml
>> 
>> 
>> The help section of your tool config should simply use a relative path to 
>> the image file ( in this case, just a a "." in front of the path to the 
>> image file )
>> 
>> .. image:: ./static/images/count_modes.png
>> :width: 500
>> 
>> I believe that's all that is necessary.
>> 
>> Greg Von Kuster
>> 
>> 
>> On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote:
>> 
>>> For one of my tool wrappers (htseq-count) in the toolshed, I point to an 
>>> image file in the Help section.  At the moment, I'm including the image in 
>>> the repository as static/imagescount_modes.png and pointing to it in the 
>>> wrapper.xml file with ".. image:: /static/images/count_modes.png".  
>>> However, the toolshed installation doesn't copy this file to the static 
>>> directory of the galaxy install (which doesn't seem like a good idea 
>>> anyway).  Is there any way for me to include a static file and then point 
>>> to that file in the help when the tool is installed automatically via the 
>>> toolshed.. Thanks.
>>> 
>>> -- 
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>> 
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> http://lists.bx.psu.edu/
>>> 
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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> 
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Re: [galaxy-dev] Toolshed - Installation of static files

[Greg Von Kuster]

Hello Lance,

Sorry this didn't work.  I've opened the following Trello card for this issue.

https://trello.com/card/toolshed-handle-images-defined-in-help-sections-of-tool-configs-contained-in-a-repository/506338ce32ae458f6d15e4b3/725

Thanks,

Greg Von Kuster


On Mar 22, 2013, at 1:50 PM, Lance Parsons wrote:

> Thanks for the quick response Greg.  I tried this and uploaded an update to 
> the testtoolshed and installed that in a test instance of Galaxy.  
> Unfortunately, it didn't seem to resolve the issue.  Galaxy still renders the 
> html with the image source pointing to the same location (e.g. 
> http://127.0.0.1:8080/static/images/count_modes.png).  This doesn't resolve.
> 
> You can try installing the htseq_count package from the testtoolshed to see 
> the issue for yourself. 
> 
> Lance
> 
> Greg Von Kuster wrote:
>> 
>> Hi Lance,
>> 
>> I answered this in your previous email - here's the answer:
>> 
>> To make this work in the tool shed, make the static directory that contains 
>> the image file a relative path in the tool config.  For example, your 
>> repository has the following structure:
>> 
>> htseq_count
>> htseq-count.xml
>> sam_fa_indices.loc.sample
>> static/
>>  images/
>>  count_modes.png
>> test-data/
>>  tool_data_table_conf.xml.sample
>>  tool_dependencies.xml
>> 
>> 
>> The help section of your tool config should simply use a relative path to 
>> the image file ( in this case, just a a "." in front of the path to the 
>> image file )
>> 
>> .. image:: ./static/images/count_modes.png
>> :width: 500
>> 
>> I believe that's all that is necessary.
>> 
>> Greg Von Kuster
>> 
>> 
>> On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote:
>> 
>>> For one of my tool wrappers (htseq-count) in the toolshed, I point to an 
>>> image file in the Help section.  At the moment, I'm including the image in 
>>> the repository as static/imagescount_modes.png and pointing to it in the 
>>> wrapper.xml file with ".. image:: /static/images/count_modes.png".  
>>> However, the toolshed installation doesn't copy this file to the static 
>>> directory of the galaxy install (which doesn't seem like a good idea 
>>> anyway).  Is there any way for me to include a static file and then point 
>>> to that file in the help when the tool is installed automatically via the 
>>> toolshed.. Thanks.
>>> 
>>> -- 
>>> Lance Parsons - Scientific Programmer
>>> 134 Carl C. Icahn Laboratory
>>> Lewis-Sigler Institute for Integrative Genomics
>>> Princeton University
>>> 
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> http://lists.bx.psu.edu/
>>> 
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>> 
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 

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Re: [galaxy-dev] Toolshed - Installation of static files

[Lance Parsons]

Thanks for the quick response Greg.  I tried this and uploaded an update 
to the testtoolshed and installed that in a test instance of Galaxy.  
Unfortunately, it didn't seem to resolve the issue.  Galaxy still 
renders the html with the image source pointing to the same location 
(e.g. http://127.0.0.1:8080/static/images/count_modes.png).  This 
doesn't resolve.


You can try installing the htseq_count package from the testtoolshed to 
see the issue for yourself.


Lance

Greg Von Kuster wrote:

Hi Lance,

I answered this in your previous email - here's the answer:

To make this work in the tool shed, make the static directory that 
contains the image file a relative path in the tool config.  For 
example, your repository has the following structure:


htseq_count 

htseq-count.xml 

sam_fa_indices.loc.sample 

static/ 

images/ 

count_modes.png 

test-data/ 

tool_data_table_conf.xml.sample 

tool_dependencies.xml 




The help section of your tool config should simply use a relative path 
to the image file ( in this case, just a a "." in front of the path to 
the image file )


.. image:: ./static/images/count_modes.png
:width: 500

I believe that's all that is necessary.

Greg Von Kuster


On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote:

For one of my tool wrappers (htseq-count) in the toolshed, I point to 
an image file in the Help section.  At the moment, I'm including the 
image in the repository as static/imagescount_modes.png and pointing 
to it in the wrapper.xml file with ".. image:: 
/static/images/count_modes.png".  However, the toolshed installation 
doesn't copy this file to the static directory of the galaxy install 
(which doesn't seem like a good idea anyway).  Is there any way for 
me to include a static file and then point to that file in the help 
when the tool is installed automatically via the toolshed.. Thanks.


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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Re: [galaxy-dev] Toolshed - Installation of static files

[Greg Von Kuster]

Hi Lance,

I answered this in your previous email - here's the answer:

To make this work in the tool shed, make the static directory that contains the 
image file a relative path in the tool config.  For example, your repository 
has the following structure:

htseq_count
htseq-count.xml
sam_fa_indices.loc.sample
static/
images/
count_modes.png
test-data/
tool_data_table_conf.xml.sample
tool_dependencies.xml


The help section of your tool config should simply use a relative path to the 
image file ( in this case, just a a "." in front of the path to the image file )

.. image:: ./static/images/count_modes.png
:width: 500

I believe that's all that is necessary.

Greg Von Kuster


On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote:

> For one of my tool wrappers (htseq-count) in the toolshed, I point to an 
> image file in the Help section.  At the moment, I'm including the image in 
> the repository as static/imagescount_modes.png and pointing to it in the 
> wrapper.xml file with ".. image:: /static/images/count_modes.png".  However, 
> the toolshed installation doesn't copy this file to the static directory of 
> the galaxy install (which doesn't seem like a good idea anyway).  Is there 
> any way for me to include a static file and then point to that file in the 
> help when the tool is installed automatically via the toolshed.. Thanks.
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Greg Von Kuster]

Hi Alex,


On Feb 4, 2013, at 10:35 AM, Bossers, Alex wrote:

> Greg and Björn, thanks for the info.
>  
> I will again review that section. Indeed a simple tool just required an xml, 
> tool script and some README. But as you guessed I was more interested in 
> complexer types; One might be the use of a bowtie2 multi mapper script we use 
> to map fastq reads to a set of databases picked from the available bowtie 
> indices within galaxy. Graphs are generated with R.
>  
> So of course the xml and wrapper scripts should be there as well as the R 
> scripts.


R scripts are defined as tool dependencies that are contained within the same 
repository.
See 
http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time


> How about bowtie2_db.lock additions?


This is defined as a 3rd-party tool dependency, and you can include a file 
named tool_dependencies.xml that defines how to install and compile it and 
ensure your appropriate repository tool can locate the compiled dependency.
See 
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories


> How to secure R and bowtie2? Just by requirements?

Can you clarify this question?


> And their licenses?

See http://wiki.galaxyproject.org/ToolShedReadmeFiles

>  
> Thanks
> Alex
>  
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Verzonden: maandag 4 februari 2013 16:25
> Aan: Bossers, Alex
> CC: galaxy-dev@lists.bx.psu.edu
> Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission
>  
> Hello Alex,
>  
> In very general terms, a repository should include everything necessary for 
> ensuring each if it's contained utilities is functionally correct when 
> installed into a local Galaxy instance.  Categories of Galaxy utilities are 
> Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy 
> workflows, 3rd-party tool dependency definitions and repository dependency 
> definitions.
>  
> I believe the content of the original tool shed wiki is mostly retained in 
> the current wiki.  The original wiki was just divided into document sections, 
> and a lot of new content has been added because of the many new tool shed 
> features that have been introduced.  The main section detailing repository 
> content it is here:  
> http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
>   This page include many related pages whose links are at the bottom of the 
> page.
>  
> It is not possible to give a precise, but general definition of what should 
> be included in all repositories because repositories can contain different 
> types of Galaxy utilities.  Each of the sections of the wiki page link above 
> describes how to include these various Galaxy utilities.  
>  
> Even Galaxy tools fall into various categories.  For example, some are very 
> simple, requiring no 3rd party tool dependencies and the tool form does not 
> use dynamically generated select lists.  These generally only require a 
> script and an XML file.  However, more complex Galaxy tools may require 
> additional supporting content to be included in the repository (e.g., a 
> tool_data_table_conf.xml.sample file. etc)
>  
> If you could provide more details about what types of utilities you are 
> building, I can steer you to the wiki pages that provide information about 
> those specific utilities.  
>  
> Thanks!
>  
> Greg Von Kuster
>  
>  
> On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:
> 
> 
> Hi All,
>  
> We are experimenting with local toolsheds for tool maintainability. On the 
> old galaxy wiki I can remember there was a short tutorial or small 
> description of the minimal requirements of a tool to be submitted to the 
> toolshed. Actually we submitted some.
> However we seem unable to retrieve the proper info from the updated wiki.
> We did find info on single tools or suites, or more special cases, but a 
> simple example/list of  how and what to include in a repository is missing 
> (at least we cannot find itmight be an issue of wrong key words)..
>  
> Anyone has an idea where to find such a document?
>  
> Thanks
> Alex
>  
>  
>  
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/
>  

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Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Björn Grüning]

Hi Alex,

for bowtie2 dependency have a look at the bismark wrapper in the main
toolshed [1]. For R please see that wiki page:

http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28script%
29

Happy hacking!
Bjoern



[1] hg clone http://toolshed.g2.bx.psu.edu/repos/bjoern-gruening/bismark



> Greg and Björn, thanks for the info.

> I will again review that section. Indeed a simple tool just required
> an xml, tool script and some README. But as you guessed I was more
> interested in complexer types; One might be the use of a bowtie2 multi
> mapper script we use to map fastq reads to a set of databases picked
> from the available bowtie indices within galaxy. Graphs are generated
> with R.
> 
>  
> 
> So of course the xml and wrapper scripts should be there as well as
> the R scripts.
> 
> How about bowtie2_db.lock additions?
> 
> How to secure R and bowtie2? Just by requirements?
> 
> And their licenses?
> 
>  
> 
> Thanks
> 
> Alex
> 
>  
> 
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Verzonden: maandag 4 februari 2013 16:25
> Aan: Bossers, Alex
> CC: galaxy-dev@lists.bx.psu.edu
> Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for
> submission
> 
> 
>  
> 
> Hello Alex,
> 
>  
> 
> 
> In very general terms, a repository should include everything
> necessary for ensuring each if it's contained utilities is
> functionally correct when installed into a local Galaxy instance.
>  Categories of Galaxy utilities are Galaxy-specific tools, proprietary
> Galaxy datatypes, exported Galaxy workflows, 3rd-party tool dependency
> definitions and repository dependency definitions.
> 
> 
>  
> 
> 
> I believe the content of the original tool shed wiki is mostly
> retained in the current wiki.  The original wiki was just divided into
> document sections, and a lot of new content has been added because of
> the many new tool shed features that have been introduced.  The main
> section detailing repository content it is here:
>  http://wiki.galaxyproject.org/Tool%
> 20Shed#The_contents_of_your_tool_shed_repository.  This page include
> many related pages whose links are at the bottom of the page.
> 
> 
>  
> 
> 
> It is not possible to give a precise, but general definition of what
> should be included in all repositories because repositories can
> contain different types of Galaxy utilities.  Each of the sections of
> the wiki page link above describes how to include these various Galaxy
> utilities.  
> 
> 
>  
> 
> 
> Even Galaxy tools fall into various categories.  For example, some are
> very simple, requiring no 3rd party tool dependencies and the tool
> form does not use dynamically generated select lists.  These generally
> only require a script and an XML file.  However, more complex Galaxy
> tools may require additional supporting content to be included in the
> repository (e.g., a tool_data_table_conf.xml.sample file. etc)
> 
> 
>  
> 
> 
> If you could provide more details about what types of utilities you
> are building, I can steer you to the wiki pages that provide
> information about those specific utilities.  
> 
> 
>  
> 
> 
> Thanks!
> 
> 
>  
> 
> 
> Greg Von Kuster
> 
> 
>  
> 
> 
>  
> 
> On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:
> 
> 
> 
> 
> Hi All,
> 
> 
>  
> 
> 
> We are experimenting with local toolsheds for tool maintainability. On
> the old galaxy wiki I can remember there was a short tutorial or small
> description of the minimal requirements of a tool to be submitted to
> the toolshed. Actually we submitted some.
> 
> 
> However we seem unable to retrieve the proper info from the updated
> wiki.
> 
> 
> We did find info on single tools or suites, or more special cases, but
> a simple example/list of  how and what to include in a repository is
> missing (at least we cannot find itmight be an issue of wrong key
> words)..
> 
> 
>  
> 
> 
> Anyone has an idea where to find such a document?
> 
> 
>  
> 
> 
> Thanks
> 
> 
> Alex
> 
> 
>  
> 
> 
>  
> 
> 
>  
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/
> 
> 
>  
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscript

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Bossers, Alex]

Greg and Björn, thanks for the info.

I will again review that section. Indeed a simple tool just required an xml, 
tool script and some README. But as you guessed I was more interested in 
complexer types; One might be the use of a bowtie2 multi mapper script we use 
to map fastq reads to a set of databases picked from the available bowtie 
indices within galaxy. Graphs are generated with R.

So of course the xml and wrapper scripts should be there as well as the R 
scripts.
How about bowtie2_db.lock additions?
How to secure R and bowtie2? Just by requirements?
And their licenses?

Thanks
Alex

Van: Greg Von Kuster [mailto:g...@bx.psu.edu]
Verzonden: maandag 4 februari 2013 16:25
Aan: Bossers, Alex
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission

Hello Alex,

In very general terms, a repository should include everything necessary for 
ensuring each if it's contained utilities is functionally correct when 
installed into a local Galaxy instance.  Categories of Galaxy utilities are 
Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 
3rd-party tool dependency definitions and repository dependency definitions.

I believe the content of the original tool shed wiki is mostly retained in the 
current wiki.  The original wiki was just divided into document sections, and a 
lot of new content has been added because of the many new tool shed features 
that have been introduced.  The main section detailing repository content it is 
here:  
http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
  This page include many related pages whose links are at the bottom of the 
page.

It is not possible to give a precise, but general definition of what should be 
included in all repositories because repositories can contain different types 
of Galaxy utilities.  Each of the sections of the wiki page link above 
describes how to include these various Galaxy utilities.

Even Galaxy tools fall into various categories.  For example, some are very 
simple, requiring no 3rd party tool dependencies and the tool form does not use 
dynamically generated select lists.  These generally only require a script and 
an XML file.  However, more complex Galaxy tools may require additional 
supporting content to be included in the repository (e.g., a 
tool_data_table_conf.xml.sample file. etc)

If you could provide more details about what types of utilities you are 
building, I can steer you to the wiki pages that provide information about 
those specific utilities.

Thanks!

Greg Von Kuster


On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:


Hi All,

We are experimenting with local toolsheds for tool maintainability. On the old 
galaxy wiki I can remember there was a short tutorial or small description of 
the minimal requirements of a tool to be submitted to the toolshed. Actually we 
submitted some.
However we seem unable to retrieve the proper info from the updated wiki.
We did find info on single tools or suites, or more special cases, but a simple 
example/list of  how and what to include in a repository is missing (at least 
we cannot find itmight be an issue of wrong key words)..

Anyone has an idea where to find such a document?

Thanks
Alex



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Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Greg Von Kuster]

Hello Alex,

In very general terms, a repository should include everything necessary for 
ensuring each if it's contained utilities is functionally correct when 
installed into a local Galaxy instance.  Categories of Galaxy utilities are 
Galaxy-specific tools, proprietary Galaxy datatypes, exported Galaxy workflows, 
3rd-party tool dependency definitions and repository dependency definitions.

I believe the content of the original tool shed wiki is mostly retained in the 
current wiki.  The original wiki was just divided into document sections, and a 
lot of new content has been added because of the many new tool shed features 
that have been introduced.  The main section detailing repository content it is 
here:  
http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository.
  This page include many related pages whose links are at the bottom of the 
page.

It is not possible to give a precise, but general definition of what should be 
included in all repositories because repositories can contain different types 
of Galaxy utilities.  Each of the sections of the wiki page link above 
describes how to include these various Galaxy utilities.  

Even Galaxy tools fall into various categories.  For example, some are very 
simple, requiring no 3rd party tool dependencies and the tool form does not use 
dynamically generated select lists.  These generally only require a script and 
an XML file.  However, more complex Galaxy tools may require additional 
supporting content to be included in the repository (e.g., a 
tool_data_table_conf.xml.sample file. etc)

If you could provide more details about what types of utilities you are 
building, I can steer you to the wiki pages that provide information about 
those specific utilities.  

Thanks!

Greg Von Kuster


On Feb 4, 2013, at 9:53 AM, Bossers, Alex wrote:

> Hi All,
>  
> We are experimenting with local toolsheds for tool maintainability. On the 
> old galaxy wiki I can remember there was a short tutorial or small 
> description of the minimal requirements of a tool to be submitted to the 
> toolshed. Actually we submitted some.
> However we seem unable to retrieve the proper info from the updated wiki.
> We did find info on single tools or suites, or more special cases, but a 
> simple example/list of  how and what to include in a repository is missing 
> (at least we cannot find itmight be an issue of wrong key words)..
>  
> Anyone has an idea where to find such a document?
>  
> Thanks
> Alex
>  
>  
>  
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Re: [galaxy-dev] Toolshed tools minimal requirments for submission

[Björn Grüning]

Hi Alex,

have a look at that page:

http://wiki.galaxyproject.org/Tool%
20Shed#The_contents_of_your_tool_shed_repository

In the near future a small sub community will review tools according to
these features. A rating system is already included in the current
toolshed.

Hope that helps a little bit.
Bjoern

> Hi All,
> We are experimenting with local toolsheds for tool maintainability. On
> the old galaxy wiki I can remember there was a short tutorial or small
> description of the minimal requirements of a tool to be submitted to
> the toolshed. Actually we submitted some.
> 
> However we seem unable to retrieve the proper info from the updated
> wiki.
> 
> We did find info on single tools or suites, or more special cases, but
> a simple example/list of  how and what to include in a repository is
> missing (at least we cannot find itmight be an issue of wrong key
> words)..
> 
>  
> 
> Anyone has an idea where to find such a document?
> 
>  
> 
> Thanks
> 
> Alex
> 
>  
> 
>  
> 
>  
> 
> 
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-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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Re: [galaxy-dev] Toolshed install 404

[Greg Von Kuster]

Hello Kyle,

The Galaxy main tool shed tracks the Galaxy-dist repo on bitbucket, and it 
looks like you are tracking Galaxy-central in your local Galaxy instance.  

Tool shed features have evolved rapidly over the past year, which has made it 
difficult to keep a stable communication layer between all revisions of Galaxy 
instances and all revisions of the tool shed.  Because of this, the Galaxy test 
tool shed has tracked the Galaxy-central repo on bitbucket and the Galaxy main 
tool shed has tracked the Galaxy-dist repo.  

The tool shed feature set is now complete enough that starting with the Galaxy 
release currently scheduled for this week, the communication layer between 
Galaxy and the tool shed will be backward compatible (to this week's release) 
going forward.

Greg Von Kuster


On Dec 16, 2012, at 11:52 PM, Kyle Ellrott wrote:

> Is anybody else getting 404 errors during toolshed installs? My instance is 
> trying to access 
> "http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=synapse_interface&owner=kellrott&changeset_revision=2925d82b84fc";
>  and gets a 404.
> 
> Kyle
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Re: [galaxy-dev] Toolshed confusion

[Greg Von Kuster]

On Dec 10, 2012, at 1:14 PM, greg wrote:

> Thanks, but I think now I'm even more confused :-(

Hmm...sorry.  I highly advise you to read the tool shed wiki as it will clear 
up a lot of your confusion.


> 
> It seems like a whole lot of the tools that are listed on the left
> panel after installing galaxy aren't actually installed.

I'm not sure to what tools you are referring here, but some Galaxy tools 
consist of 2 components ( a UI based on Cheetah, and a script that has no 
requirements ) while others have a 3rd component ( a 3rd-party dependency ).  
When you clone the Galaxy distribution, those tools that require dependencies 
must have those dependencies manually installed and defined on a path in such a 
way that the Galaxy user ( the account used to start the Galaxy server ) can 
find them.  This has always been the case, and has nothing to do with the tool 
shed.

However, the tool shed improves this process for those repositories that you 
install into your Galaxy instance that include tools and defined dependencies 
for them.


> 
> For example FastQC.  Then I do see FastQC in the tool shed, but it
> seems like when I go to install it, it will create its own entry on
> the left panel and not fix the FastQC tool that's already there.


These are 2 different tools, although they are named similarly.  You'll notice, 
though, that they have different IDs.  So installing a tool from the tool shed 
will not fix or replace an existing tool with the same name in a Galaxy 
instance into which it was installed.



> 
> So if I install everything I can from the tool shed I'll still be left
> with a whole lot of broken tools in the left panel?


Possibly - again, it is the responsibility of the repository owner to ensure 
the tools are functionally correct when installed into Galaxy.  A commission is 
in place to review and approve the contents of repositories on the main Galaxy 
tool shed, but it has not yet undertaken this endeavor.


> 
> (I guess the tool shed is just for new tools, and not to fix the ones
> already listed in Galaxy.  

Any tools included in the Galaxy distribution does not need "fixing".  At most 
they need a dependency to be manually installed.  See the tool dependencies 
page in the Galaxy wiki for details.  It's available here:

http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies


> Would it make sense to stop including tool
> links on the left panel that aren't bundled with Galaxy, and then let
> the toolshed add them in?)
> 

Not sure what you mean here.

> -Greg
> 
> On Mon, Dec 10, 2012 at 11:16 AM, Greg Von Kuster  wrote:
>> Hi Greg,
>> 
>> In case you haven't found it, the tool shed wiki provides a lot of 
>> information.  It's available at  http://wiki.galaxyproject.org/Tool%20Shed
>> 
>> 
>> On Dec 10, 2012, at 10:59 AM, greg wrote:
>> 
>>> Hi guys,
>>> 
>>> I have my fresh galaxy install on our cluster and now I'm trying to
>>> figure out which tools are missing and how to install them.
>>> 
>>> I just came across the toolshed so now I'm really confused.
>>> 
>>> Question 1:
>>> Can I install EVERY tool I need from the tool shed or are there some
>>> things I need to install manually first like R, Samtools, etc?  How do
>>> I know what to install from where?
>> 
>> The intent of the tool shed is to share Galaxy utilities (  tools, exported 
>> workflows, proprietary datatypes, etc) developed by many contributors in the 
>> Galaxy community.  The tool shed provides a very rich set of features that 
>> enhance those provided by Galaxy itself.  In this way it complements galaxy. 
>>  For example, the tool shed provides features that allow tool developers to 
>> include information within their tool shed repository to automatically 
>> install ( and possibly compile ) tool dependencies for tools within the 
>> repository.
>> 
>> However, it is up to the repository owner (the community contributor ) to 
>> use tool shed features like this.  So some repositories include tools that 
>> will install dependencies, while others require manual dependency 
>> installation.
>> 
>> The core Galaxy development team is in the process of migrating tools from 
>> the Galaxy distribution to the main Galaxy tool shed.  Tools that have been 
>> migrated in this way are all contained in repositories with the owner 
>> "devteam".  If these repositories include tools, then they will have 
>> dependencies defined for them, so the dependencies will be installed along 
>> with the repositories.
>> 
>> 
>>> 
>>> Question 2:
>>> Is it preferable to use the toolshed whenever possible, or it is not
>>> fully developed yet?
>> 
>> 
>> It is preferable to use the tool shed whenever possible, but additional 
>> features will continue to be added.   This does not imply that you have to 
>> wait for additional features before using the tool shed.
>> 
>> 
>>> 
>>> Thanks,
>>> 
>>> Greg
>>> ___
>>> Please keep all replies on the list by usi

Re: [galaxy-dev] Toolshed confusion

[greg]

Thanks, but I think now I'm even more confused :-(

It seems like a whole lot of the tools that are listed on the left
panel after installing galaxy aren't actually installed.

For example FastQC.  Then I do see FastQC in the tool shed, but it
seems like when I go to install it, it will create its own entry on
the left panel and not fix the FastQC tool that's already there.

So if I install everything I can from the tool shed I'll still be left
with a whole lot of broken tools in the left panel?

(I guess the tool shed is just for new tools, and not to fix the ones
already listed in Galaxy.  Would it make sense to stop including tool
links on the left panel that aren't bundled with Galaxy, and then let
the toolshed add them in?)

-Greg

On Mon, Dec 10, 2012 at 11:16 AM, Greg Von Kuster  wrote:
> Hi Greg,
>
> In case you haven't found it, the tool shed wiki provides a lot of 
> information.  It's available at  http://wiki.galaxyproject.org/Tool%20Shed
>
>
> On Dec 10, 2012, at 10:59 AM, greg wrote:
>
>> Hi guys,
>>
>> I have my fresh galaxy install on our cluster and now I'm trying to
>> figure out which tools are missing and how to install them.
>>
>> I just came across the toolshed so now I'm really confused.
>>
>> Question 1:
>> Can I install EVERY tool I need from the tool shed or are there some
>> things I need to install manually first like R, Samtools, etc?  How do
>> I know what to install from where?
>
> The intent of the tool shed is to share Galaxy utilities (  tools, exported 
> workflows, proprietary datatypes, etc) developed by many contributors in the 
> Galaxy community.  The tool shed provides a very rich set of features that 
> enhance those provided by Galaxy itself.  In this way it complements galaxy.  
> For example, the tool shed provides features that allow tool developers to 
> include information within their tool shed repository to automatically 
> install ( and possibly compile ) tool dependencies for tools within the 
> repository.
>
> However, it is up to the repository owner (the community contributor ) to use 
> tool shed features like this.  So some repositories include tools that will 
> install dependencies, while others require manual dependency installation.
>
> The core Galaxy development team is in the process of migrating tools from 
> the Galaxy distribution to the main Galaxy tool shed.  Tools that have been 
> migrated in this way are all contained in repositories with the owner 
> "devteam".  If these repositories include tools, then they will have 
> dependencies defined for them, so the dependencies will be installed along 
> with the repositories.
>
>
>>
>> Question 2:
>> Is it preferable to use the toolshed whenever possible, or it is not
>> fully developed yet?
>
>
> It is preferable to use the tool shed whenever possible, but additional 
> features will continue to be added.   This does not imply that you have to 
> wait for additional features before using the tool shed.
>
>
>>
>> Thanks,
>>
>> Greg
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>> and other Galaxy lists, please use the interface at:
>>
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>
>
> Greg Von Kuster
>

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Re: [galaxy-dev] Toolshed confusion

[Greg Von Kuster]

Hi Greg,

In case you haven't found it, the tool shed wiki provides a lot of information. 
 It's available at  http://wiki.galaxyproject.org/Tool%20Shed


On Dec 10, 2012, at 10:59 AM, greg wrote:

> Hi guys,
> 
> I have my fresh galaxy install on our cluster and now I'm trying to
> figure out which tools are missing and how to install them.
> 
> I just came across the toolshed so now I'm really confused.
> 
> Question 1:
> Can I install EVERY tool I need from the tool shed or are there some
> things I need to install manually first like R, Samtools, etc?  How do
> I know what to install from where?

The intent of the tool shed is to share Galaxy utilities (  tools, exported 
workflows, proprietary datatypes, etc) developed by many contributors in the 
Galaxy community.  The tool shed provides a very rich set of features that 
enhance those provided by Galaxy itself.  In this way it complements galaxy.  
For example, the tool shed provides features that allow tool developers to 
include information within their tool shed repository to automatically install 
( and possibly compile ) tool dependencies for tools within the repository. 

However, it is up to the repository owner (the community contributor ) to use 
tool shed features like this.  So some repositories include tools that will 
install dependencies, while others require manual dependency installation.

The core Galaxy development team is in the process of migrating tools from the 
Galaxy distribution to the main Galaxy tool shed.  Tools that have been 
migrated in this way are all contained in repositories with the owner 
"devteam".  If these repositories include tools, then they will have 
dependencies defined for them, so the dependencies will be installed along with 
the repositories.


> 
> Question 2:
> Is it preferable to use the toolshed whenever possible, or it is not
> fully developed yet?


It is preferable to use the tool shed whenever possible, but additional 
features will continue to be added.   This does not imply that you have to wait 
for additional features before using the tool shed.


> 
> Thanks,
> 
> Greg
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Greg Von Kuster


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Re: [galaxy-dev] ToolShed README files, was: Blast2GO local instance

[Peter Cock]

On Thursday, September 27, 2012, Greg Von Kuster wrote:

> Hello Peter,
>
> My recent change set 7753:c28c5f906c6b added the ability to view a tool
> shed repository's README file from the pop-up menu on pages in the tool
> shed repository as well as in the Galaxy Admin UUI for installed
> repositories.  Since many of these README files are rather large, I needed
> to display them on a separate page, hence the need for the new Repository
> Actions popup menu "View README" item.
>
>
Great - and thank you for the line wrapping change too - I look forward to
seeing these refinements in action :)

Peter
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Re: [galaxy-dev] ToolShed README files, was: Blast2GO local instance

[Greg Von Kuster]

Hi Peter,

I've handled this request in change set revision 7761:9972ac6ee91d, which will 
be included in the next Galaxy release scheduled for about 10 days from now.

Thanks!

Greg Von Kuster


On Aug 28, 2012, at 9:48 AM, Peter Cock wrote:

> P.S. It would be nice to automatically line wrap the "Detailed
> description", as in many cases the raw text doesn't do this.
> For example, fubar's clustalw tool.


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Re: [galaxy-dev] ToolShed README files, was: Blast2GO local instance

[Greg Von Kuster]

Hello Peter,

My recent change set 7753:c28c5f906c6b added the ability to view a tool shed 
repository's README file from the pop-up menu on pages in the tool shed 
repository as well as in the Galaxy Admin UUI for installed repositories.  
Since many of these README files are rather large, I needed to display them on 
a separate page, hence the need for the new Repository Actions popup menu "View 
README" item.  



On Aug 28, 2012, at 9:48 AM, Peter Cock wrote:

> 
>> This works only if
>> using the tool shed installation process, so for example, if
>> installing the venn_list repository, clicking "Install to local Galaxy"
>> in this screenshot:
> 
> Ah. I see now it just isn't doing what I expected - apologies for
> any misdirection.
> 
> I had assumed if a README file was present, it would be shown
> prominent while browsing on the ToolShed. On closer examination
> of an example repository where there is a file named exactly
> 'README' (e.g. fubar's clustalw tool) that isn't shown either.
> 
> Is there any reason not to show the contents of the README file
> (using the discussed name variations) on the main ToolShed
> repository view, e.g. under a new yellow section header?

> 






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Re: [galaxy-dev] toolshed upload problem

[Greg Von Kuster]

Hi David,

I committed a fix for this issue in changeset 7662:c4ced3262d0d, which is 
currently available only in the Galaxy central repository.  The fix will be 
available in the next Galaxy release scheduled for the end of next week.

Thanks for reporting this problem, and sorry for the inconvenience.

Greg Von Kuster

On Sep 12, 2012, at 6:16 PM, David Hoover wrote:

> I've created a repository in the test toolshed and tried uploading gzipped 
> tarballs with all files required.  I have several tool config files (.xml) 
> wrapping a single python script with some tool-data dependencies.
> 
> If I upload a single tool config file with the dependencies, everything is 
> ok.  However, if I try uploading more than one config file at a time, it 
> complains with the error message for all but one of the config files:
> 
> *.xml - This file requires an entry for "'gatk2_picard_indexes'" in the 
> tool_data_table_conf.xml file. Upload a file named 
> tool_data_table_conf.xml.sample to the repository that includes the required 
> entry to correct this error.
> 
> The tool_data_table_conf.xml.sample file already exists within the tarball.  
> Nothing changes if I upload the file separately.
> 
> Any ideas?
> 
> David Hoover
> Helix Systems Staff
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Re: [galaxy-dev] toolshed upload problem

[Greg Von Kuster]

Hi David,

Can you send me your tarball?

Thanks,

Greg Von Kuster


On Sep 12, 2012, at 6:16 PM, David Hoover wrote:

> I've created a repository in the test toolshed and tried uploading gzipped 
> tarballs with all files required.  I have several tool config files (.xml) 
> wrapping a single python script with some tool-data dependencies.
> 
> If I upload a single tool config file with the dependencies, everything is 
> ok.  However, if I try uploading more than one config file at a time, it 
> complains with the error message for all but one of the config files:
> 
> *.xml - This file requires an entry for "'gatk2_picard_indexes'" in the 
> tool_data_table_conf.xml file. Upload a file named 
> tool_data_table_conf.xml.sample to the repository that includes the required 
> entry to correct this error.
> 
> The tool_data_table_conf.xml.sample file already exists within the tarball.  
> Nothing changes if I upload the file separately.
> 
> Any ideas?
> 
> David Hoover
> Helix Systems Staff
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Re: [galaxy-dev] Toolshed is not starting + patch

[Greg Von Kuster]

Hi Bjorn,

The main Galaxy tool shed is tracking the Galaxy-dist repository.  Per requests 
from the Galaxy community, it no longer tracks Galaxy-central.

Greg Von Kuster

On Sep 10, 2012, at 12:25 PM, Björn Grüning wrote:

> Hi,
> 
> the toolshed is not starting with the latest galaxy-central version.
> Attached is a small patch to solve that problem.
> 
> Cheers,
> Bjoern
> 
> -- 
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
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Re: [galaxy-dev] ToolShed enhancement for repository lists

[Greg Von Kuster]

I've added this new feature in changeset 7556:c87370c5340d, which will be 
available in the tool shed the next time it is updated.  I'm making every 
attempt to have the tool shed code base track the Galaxy distribution releases, 
so the tool shed will probably not be updated until the next release to the 
galaxy-dist repository.

Greg Von Kuster


On Aug 22, 2012, at 9:19 AM, Peter Cock wrote:

> Hi all,
> 
> This is an idea I mentioned to Dannon (off list during discussion
> about moving the NCBI BLAST+ wrappers to the Tool Shed), and
> he seemed positive about it.
> 
> Currently the left hand pane of the ToolShed (once logged in)
> looks like this:
> 
> Search
> * Search for valid tools
> * Search for workflows
> Repositories
> * Browse by category
> * Browse my repositories
> * Browse my invalid tools
> * Create new repository
> 
> I would find it useful to add another entry listing those repositories
> where I have contributor rights. This could be included under the
> existing "Browse my repositories", but perhaps a separate entry
> is better - if anyone has a concise description for this (so far
> I've not come up with a short way of phrasing this).
> 
> Should I file this as an enhancement issue on BitBucket?
> 
> Regards,
> 
> Peter
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Re: [galaxy-dev] ToolShed README files, was: Blast2GO local instance

[Peter Cock]

On Tue, Aug 28, 2012 at 2:30 PM, Greg Von Kuster  wrote:
> HI Peter,
>
> On Aug 23, 2012, at 9:52 AM, Peter Cock wrote:
>
>> Hi Greg,
>>
>> Could you include .txt on the list of README
>> filenames looked for by the ToolShed as you said please?
>>
>> I've just checked and it isn't working at the moment. e.g. blast2go,
>> seq_rename, clinod, venn_list, ... - in fact most of my tools :(
>>
>> Thanks,
>>
>> Peter
>
> I've checked each of your listed repositories and the information
> in each of your .txt files is in fact displayed
> when installing into a local Galaxy instance.

That's good - so the wiki needs updating:
http://wiki.g2.bx.psu.edu/Tool%20Shed

> This works only if
> using the tool shed installation process, so for example, if
> installing the venn_list repository, clicking "Install to local Galaxy"
> in this screenshot:

Ah. I see now it just isn't doing what I expected - apologies for
any misdirection.

I had assumed if a README file was present, it would be shown
prominent while browsing on the ToolShed. On closer examination
of an example repository where there is a file named exactly
'README' (e.g. fubar's clustalw tool) that isn't shown either.

Is there any reason not to show the contents of the README file
(using the discussed name variations) on the main ToolShed
repository view, e.g. under a new yellow section header?

Thanks,

Peter

P.S. It would be nice to automatically line wrap the "Detailed
description", as in many cases the raw text doesn't do this.
For example, fubar's clustalw tool.
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Re: [galaxy-dev] Toolshed: disabling registering

[Greg Von Kuster]

It's implied, although not clearly stated in the wiki.  The User component is 
the same code for both applications, so User component features that are 
available in Galaxy are generally available in the tool shed as well.  I'm soon 
going to be making some major changes to the tool shed wiki, so I can clarify 
this.

Thanks Joachim!


On Aug 3, 2012, at 3:20 AM, Joachim Jacob wrote:

> Thanks, works like a charm.
> 
> Could it be that this is not documented? Where can I find those options? 
> (perhaps in the code?) Then I can perhaps add it to the wiki.
> 
> 
> Kind regards,
> 
> Joachim Jacob, PhD
> 
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
> 
> On 08/02/2012 03:37 PM, Greg Von Kuster wrote:
>> allow_user_creation = False
> 


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Re: [galaxy-dev] Toolshed: disabling registering

[Joachim Jacob]

Thanks, works like a charm.

Could it be that this is not documented? Where can I find those options? 
(perhaps in the code?) Then I can perhaps add it to the wiki.



Kind regards,

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 08/02/2012 03:37 PM, Greg Von Kuster wrote:

allow_user_creation = False


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Re: [galaxy-dev] Toolshed: disabling registering

[Greg Von Kuster]

Hi Joachim,

Yes, add the following to the [app:main] section of your community_wsgi.ini 
file.

allow_user_creation = False


On Aug 2, 2012, at 4:51 AM, Joachim Jacob wrote:

> Hi,
> 
> Can I disable the account creation by users in our Galaxy tool shed?
> 
> Joachim
> 
> -- 
> Joachim Jacob, PhD
> 
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
> 
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Re: [galaxy-dev] Toolshed error with proprietary datatypes

[Greg Von Kuster]

Hi Bjoren,

What revision are you seeing this in?  I don't think this issues exists in 
Galaxy central's tip, but let me know.

Thanks!

Greg

On Jun 8, 2012, at 10:44 AM, Björn Grüning wrote:

> Hi Greg,
> 
> thanks! I can confirm that it is working now. I can upload new
> datatypes.
> What is not working is the update of such tools from the toolshed.
> I get the following error.
> 
> URL:
> http://localhost/toolshed/repository/check_for_updates?galaxy_url=http://localhost/&name=molecule_datatypes&owner=admin&changeset_revision=2a638740087d&webapp=galaxy&no_reset=true
> Module paste.exceptions.errormiddleware:143 in __call__
>>> app_iter = self.application(environ, start_response)
> Module paste.debug.prints:98 in __call__
>>> environ, self.app)
> Module paste.wsgilib:539 in intercept_output
>>> app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__
>>> return self.application(environ, start_response)
> Module paste.httpexceptions:632 in __call__
>>> return self.application(environ, start_response)
> Module galaxy.web.framework.base:160 in __call__
>>> body = method( trans, **kwargs )
> Module galaxy.webapps.community.controllers.repository:684 in
> check_for_updates
>>> url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
> UnboundLocalError: local variable 'latest_ctx' referenced before
> assignment
> 
> Removing and installing works fine.
> If you need more information to track that bug done, let me know.
> 
> Cheers,
> Bjoern
> 
> 
>> Hello Bjoern,
>> 
>> This should be resolved in change set 7211:16a93eb6eaf6, which is available 
>> from our central repository.  Thanks for reporting this, and please let me 
>> know if you encounter additional issues.
>> 
>> Greg Von Kuster
>> 
>> 
>> On May 26, 2012, at 10:51 AM, Björn Grüning wrote:
>> 
>>> Hi,
>>> 
>>> has anyone encountered that problem or has an idea how to solve it?
>>> 
>>> Traceback (most recent call last):
>>> File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
>>> app_factory
>>>   app = UniverseApplication( global_conf = global_conf, **kwargs )
>>> File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
>>>   self.installed_repository_manager.load_proprietary_datatypes()
>>> File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
>>> 26, in load_proprietary_datatypes
>>>   load_datatype_items( self.app, tool_shed_repository,
>>> relative_install_dir )
>>> File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036,
>>> in load_datatype_items
>>>   app.datatypes_registry.load_datatype_converters( app.toolbox,
>>> installed_repository_dict=repository_dict, deactivate=deactivate )
>>> AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
>>> 
>>> All files are in one repository ... xml, the python-class und the
>>> converters. I was able to successfully upload it to our test-toolshed
>>> but after installing it (also successfully) galaxy is not able to start.
>>> Also the converters are recognised as tools in the toolshed is that
>>> intended?
>>> 
>>> Thanks!
>>> Bjoern
>>> 
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>> 
> 
> -- 
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> 


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Re: [galaxy-dev] Toolshed error with proprietary datatypes

[Björn Grüning]

Hi Greg,

thanks! I can confirm that it is working now. I can upload new
datatypes.
What is not working is the update of such tools from the toolshed.
I get the following error.

URL:
http://localhost/toolshed/repository/check_for_updates?galaxy_url=http://localhost/&name=molecule_datatypes&owner=admin&changeset_revision=2a638740087d&webapp=galaxy&no_reset=true
Module paste.exceptions.errormiddleware:143 in __call__
>>  app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
>>  body = method( trans, **kwargs )
Module galaxy.webapps.community.controllers.repository:684 in
check_for_updates
>>  url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() )
UnboundLocalError: local variable 'latest_ctx' referenced before
assignment

Removing and installing works fine.
If you need more information to track that bug done, let me know.

Cheers,
Bjoern


> Hello Bjoern,
> 
> This should be resolved in change set 7211:16a93eb6eaf6, which is available 
> from our central repository.  Thanks for reporting this, and please let me 
> know if you encounter additional issues.
> 
> Greg Von Kuster
> 
> 
> On May 26, 2012, at 10:51 AM, Björn Grüning wrote:
> 
> > Hi,
> > 
> > has anyone encountered that problem or has an idea how to solve it?
> > 
> > Traceback (most recent call last):
> >  File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
> > app_factory
> >app = UniverseApplication( global_conf = global_conf, **kwargs )
> >  File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
> >self.installed_repository_manager.load_proprietary_datatypes()
> >  File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
> > 26, in load_proprietary_datatypes
> >load_datatype_items( self.app, tool_shed_repository,
> > relative_install_dir )
> >  File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036,
> > in load_datatype_items
> >app.datatypes_registry.load_datatype_converters( app.toolbox,
> > installed_repository_dict=repository_dict, deactivate=deactivate )
> > AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
> > 
> > All files are in one repository ... xml, the python-class und the
> > converters. I was able to successfully upload it to our test-toolshed
> > but after installing it (also successfully) galaxy is not able to start.
> > Also the converters are recognised as tools in the toolshed is that
> > intended?
> > 
> > Thanks!
> > Bjoern
> > 
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> > 
> >  http://lists.bx.psu.edu/
> 

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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Re: [galaxy-dev] Toolshed error with proprietary datatypes

[Greg Von Kuster]

Hello Bjoern,

This should be resolved in change set 7211:16a93eb6eaf6, which is available 
from our central repository.  Thanks for reporting this, and please let me know 
if you encounter additional issues.

Greg Von Kuster


On May 26, 2012, at 10:51 AM, Björn Grüning wrote:

> Hi,
> 
> has anyone encountered that problem or has an idea how to solve it?
> 
> Traceback (most recent call last):
>  File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
> app_factory
>app = UniverseApplication( global_conf = global_conf, **kwargs )
>  File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
>self.installed_repository_manager.load_proprietary_datatypes()
>  File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
> 26, in load_proprietary_datatypes
>load_datatype_items( self.app, tool_shed_repository,
> relative_install_dir )
>  File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036,
> in load_datatype_items
>app.datatypes_registry.load_datatype_converters( app.toolbox,
> installed_repository_dict=repository_dict, deactivate=deactivate )
> AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
> 
> All files are in one repository ... xml, the python-class und the
> converters. I was able to successfully upload it to our test-toolshed
> but after installing it (also successfully) galaxy is not able to start.
> Also the converters are recognised as tools in the toolshed is that
> intended?
> 
> Thanks!
> Bjoern
> 
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Toolshed error with proprietary datatypes

[Björn Grüning]

Hi Greg,

> What version of Galaxy are you using?  

I could reproduce it with latest galaxy-central 7202:f4c4ba7be3d1. Same
error and the converters are displayed in the tool menu.
I will send you my tarball off the list, if you are interested in
reproducing.

Thanks,
Bjoern

> Your code base should be tracking the galaxy-central repository on bitbucket 
> in order to use  the tool shed with your local Galaxy instance. 
> The galaxy-central repo is currently around 7201:62bdb265d300, and you can 
> see the version you are running by typing the 
> following in your Galaxy installation directory.
> 
> %hg heads
> 
> I believe this behavior will be resolved if you update to the latest code, 
> but let me know if you continue to bump into problems.
> 
> Thanks,
> 
> Greg Von Kuster
> 
> On May 26, 2012, at 10:51 AM, Björn Grüning wrote:
> 
> > Hi,
> > 
> > has anyone encountered that problem or has an idea how to solve it?
> > 
> > Traceback (most recent call last):
> > File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
> > app_factory
> >   app = UniverseApplication( global_conf = global_conf, **kwargs )
> > File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
> >   self.installed_repository_manager.load_proprietary_datatypes()
> > File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
> > 26, in load_proprietary_datatypes
> >   load_datatype_items( self.app, tool_shed_repository,
> > relative_install_dir )
> > File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036,
> > in load_datatype_items
> >   app.datatypes_registry.load_datatype_converters( app.toolbox,
> > installed_repository_dict=repository_dict, deactivate=deactivate )
> > AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
> > 
> > All files are in one repository ... xml, the python-class und the
> > converters. I was able to successfully upload it to our test-toolshed
> > but after installing it (also successfully) galaxy is not able to start.
> > Also the converters are recognised as tools in the toolshed is that
> > intended?
> > 
> > Thanks!
> > Bjoern
> > 
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> > 
> > http://lists.bx.psu.edu/
> 


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Re: [galaxy-dev] Toolshed error with proprietary datatypes

[Greg Von Kuster]

Hello Bjoern,

What version of Galaxy are you using?  Your code base should be tracking the 
galaxy-central repository on bitbucket in order to use  the tool shed with your 
local Galaxy instance.  The galaxy-central repo is currently around 
7201:62bdb265d300, and you can see the version you are running by typing the 
following in your Galaxy installation directory.

%hg heads

I believe this behavior will be resolved if you update to the latest code, but 
let me know if you continue to bump into problems.

Thanks,

Greg Von Kuster

On May 26, 2012, at 10:51 AM, Björn Grüning wrote:

> Hi,
> 
> has anyone encountered that problem or has an idea how to solve it?
> 
> Traceback (most recent call last):
> File "/home/ctb/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in
> app_factory
>   app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/home/ctb/galaxy-dist/lib/galaxy/app.py", line 64, in __init__
>   self.installed_repository_manager.load_proprietary_datatypes()
> File "/home/ctb/galaxy-dist/lib/galaxy/tool_shed/__init__.py", line
> 26, in load_proprietary_datatypes
>   load_datatype_items( self.app, tool_shed_repository,
> relative_install_dir )
> File "/home/ctb/galaxy-dist/lib/galaxy/util/shed_util.py", line 1036,
> in load_datatype_items
>   app.datatypes_registry.load_datatype_converters( app.toolbox,
> installed_repository_dict=repository_dict, deactivate=deactivate )
> AttributeError: 'UniverseApplication' object has no attribute 'toolbox'
> 
> All files are in one repository ... xml, the python-class und the
> converters. I was able to successfully upload it to our test-toolshed
> but after installing it (also successfully) galaxy is not able to start.
> Also the converters are recognised as tools in the toolshed is that
> intended?
> 
> Thanks!
> Bjoern
> 
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> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
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Re: [galaxy-dev] Toolshed initial upload errors

[Paul-Michael Agapow]

And the saga continues. For those who came in late - I've installed a local 
toolshed, which allows me to create repositories, but every time  I attempt to 
upload files, it errors out with "TypeError: array item must be char". Working 
off the latest Galaxy bleeding edge copy has failed to fix this. Things I've 
looked at:

- Initial os was CentOS (4?), Mercurial 2.1.2, Python 2.6.4, with sqlite. Also 
tried with Ubuntu 10.04, Python 2.7.
- The Mercurial and Python I used was is local to the account I was working in, 
so maybe the toolshed was getting confused with another version. Nope - there's 
no hg on the system. Galaxy seems to be calling the right Python (libraries)
- This happens with plain text and binary files. I haven't attempted to upload 
an archive yet
- Figured there could still be something peculiar to my environment, so 
installed Galaxy on a fresh server I had elsewhere (the Ubuntu one listed 
above). Nope - exactly the same error.
- As there are some reported issues of Windows file names with Unicode under 
Mercurial, and I'm uploading from a Windows machine, I used a Mac to create a 
repo and add a file. Nope, same behaviour.
-  Further investigations reveal that the files appear to be in the repo 
(database/community_files). The error occurs in the middle of Mercurial, in 
manifest.py where it attempts to coerce a Unicode string into a character 
array. The Cistrome galaxy fork 
(https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py)
 mentions occasional similar errors.
- Wondered if it was specific to my db setup. Used Postgres instead, same 
behaviour.
- The only changes I make to community_wsgi.ini are setting the host and port, 
setting the database details, and setting the admin user

Frankly, I'm fresh out of inspiration. There must be something I'm consistently 
doing (or not doing). Any suggestions - or wild-ass guesses - where to look 
next?


Paul Agapow (paul-michael.aga...@hpa.org.uk)
Bioinformatics, Health Protection Agency

  
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Re: [galaxy-dev] Toolshed - 502 Bad Gateway error

[Nate Coraor]

Hi Graham,

Thanks for the heads up.  It's been fixed.

--nate

On May 2, 2012, at 9:39 AM, graham etherington (TSL) wrote:

> Hi,
> The Galaxy Toolshed is giving a 502 Bad Gateway error. Is there a problem
> with it at the moment?
> If so, is it just a matter of restarting it or is there a likelihood of it
> being down for a while?
> Cheers,
> Graham
> 
> Dr. Graham Etherington
> Bioinformatics Support Officer,
> The Sainsbury Laboratory,
> Norwich Research Park,
> Norwich NR4 7UH.
> UK
> Tel: +44 (0)1603 450601
> 
> 
> 
> 
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Re: [galaxy-dev] Toolshed initial upload errors

[Greg Von Kuster]

Hi Paul,

The use of mercurial eggs for all tool shed mercurial related actions is now 
available in our central repository in change set 7102:c8f4f73e9199.  This will 
be available in the dist repository with the next release, which I believe will 
be coming soon.  If you're tracking the central repository, updating will 
hopefully solve the problems you were seeing.

Thanks!

Greg Von Kuster

On Apr 20, 2012, at 7:39 AM, Paul-Michael Agapow wrote:

> Thanks Greg,
> 
> It's a puzzling one alright. Looking forward to testing the new version, if 
> only because I've run out of ideas on where to look.
> 
> Cheers
> 
> p
> 
> 
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Health Protection Agency
> 
> -Original Message-
> From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Sent: 19 April 2012 22:47
> To: Paul-Michael Agapow
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> Subject: Re: [galaxy-dev] Toolshed initial upload errors
> 
> Paul,
> 
> Sorry to see you're still experiencing problems.  Based on the issues you've 
> encountered (as well as one or two others recently) I've spent some time 
> re-working things to eliminate the need for installing mercurial to use a 
> local tool shed.  We will build eggs for the mercurial package for the 
> various versions of Python supported by Galaxy and include them in the 
> distribution.  
> 
> I'm pretty close to having this finished, so it is likely that this will be 
> available early next week.  
> 
> I'm not sure if this will fix the problems you're seeing, but at least it 
> will eliminate one of the variables.
> 
> Greg Von Kuster
> 
> On Apr 19, 2012, at 5:02 AM, Paul-Michael Agapow wrote:
> 
>> [For those who came in late - I've installed a local toolshed, which allows 
>> me to create repositories, but every time  I attempt to upload files, it 
>> errors out with "TypeError: array item must be char". For those who come 
>> after me, here's what I worked out thus far.]
>> 
>> Greg asked:
>> 
>>> Since you've tried uploading various files with no success, the problem is 
>>> likely
>>> to be caused by something specific to your environment - possibly the 
>>> version of
>>> the mercurial package you're using.  What version of Python are you 
>>> running, and
>>> what version of the mercurial package do you have installed with it?  Also, 
>>> what
>>> version of Galaxy do you have, and what database / version are you using?
>> 
>> We're CentOS, an older flavour (4), but my Mercurial is up to data (2.1.2). 
>> Python 2.6.4, Galaxy is 6799:40f1816d6857 (grabbed it fresh last week for 
>> testing), running it with sqlite. However, the Mercurial is actually 
>> installed local to the account I'm using, so I wonder if the toolshed is 
>> getting confused with another version, although hg doesn't seem to be 
>> installed on the system.
>> 
>> Further investigations reveal that the files appear to be in the repo 
>> (database/community_files). The error manifest in the middle of Mercurial, 
>> in manifest.py where it attempts to coerce a Unicode string into a character 
>> array. (As there are some reported issues of Windows file names with Unicode 
>> under Mercurial, and I'm uploading from a Windows machine, I used a Mac to 
>> create a repo and add a file. Nope, same behaviour.) The Cistrome galaxy 
>> fork 
>> (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py)
>>  mentions occasional similar errors.
>> 
>> I check the Mercurial installation:
>> 
>> % hg --version
>> Mercurial Distributed SCM (version 2.1.2+10-4d875bb546dc)
>> ...
>> % hg debuginstall
>> Checking encoding (UTF-8)...
>> Checking installed modules 
>> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial)...
>> Checking templates 
>> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial/templates)...
>> Checking commit editor...
>> Checking username...
>> No problems detected
>> 
>> (Actually, I was missing a username and a user ~/.hgrc file. But making 
>> that, it passes. Error still persists.)
>> 
>> Work continues.
>> 
>> 
>> Paul Agapow (paul-michael.aga...@hpa.org.uk)
>> Bioinformatics, Health Protection Agency
>> 
>> -
>> 

Re: [galaxy-dev] Toolshed initial upload errors

[Greg Von Kuster]

Paul,

Sorry to see you're still experiencing problems.  Based on the issues you've 
encountered (as well as one or two others recently) I've spent some time 
re-working things to eliminate the need for installing mercurial to use a local 
tool shed.  We will build eggs for the mercurial package for the various 
versions of Python supported by Galaxy and include them in the distribution.  

I'm pretty close to having this finished, so it is likely that this will be 
available early next week.  

I'm not sure if this will fix the problems you're seeing, but at least it will 
eliminate one of the variables.

Greg Von Kuster

On Apr 19, 2012, at 5:02 AM, Paul-Michael Agapow wrote:

> [For those who came in late - I've installed a local toolshed, which allows 
> me to create repositories, but every time  I attempt to upload files, it 
> errors out with "TypeError: array item must be char". For those who come 
> after me, here's what I worked out thus far.]
> 
> Greg asked:
> 
>> Since you've tried uploading various files with no success, the problem is 
>> likely
>> to be caused by something specific to your environment - possibly the 
>> version of
>> the mercurial package you're using.  What version of Python are you running, 
>> and
>> what version of the mercurial package do you have installed with it?  Also, 
>> what
>> version of Galaxy do you have, and what database / version are you using?
> 
> We're CentOS, an older flavour (4), but my Mercurial is up to data (2.1.2). 
> Python 2.6.4, Galaxy is 6799:40f1816d6857 (grabbed it fresh last week for 
> testing), running it with sqlite. However, the Mercurial is actually 
> installed local to the account I'm using, so I wonder if the toolshed is 
> getting confused with another version, although hg doesn't seem to be 
> installed on the system.
> 
> Further investigations reveal that the files appear to be in the repo 
> (database/community_files). The error manifest in the middle of Mercurial, in 
> manifest.py where it attempts to coerce a Unicode string into a character 
> array. (As there are some reported issues of Windows file names with Unicode 
> under Mercurial, and I'm uploading from a Windows machine, I used a Mac to 
> create a repo and add a file. Nope, same behaviour.) The Cistrome galaxy fork 
> (https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py)
>  mentions occasional similar errors.
> 
> I check the Mercurial installation:
> 
> % hg --version
> Mercurial Distributed SCM (version 2.1.2+10-4d875bb546dc)
> ...
> % hg debuginstall
> Checking encoding (UTF-8)...
> Checking installed modules 
> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial)...
> Checking templates 
> (/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial/templates)...
> Checking commit editor...
> Checking username...
> No problems detected
> 
> (Actually, I was missing a username and a user ~/.hgrc file. But making that, 
> it passes. Error still persists.)
> 
> Work continues.
> 
> 
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Health Protection Agency
> 
> -
> **
> The information contained in the EMail and any attachments is
> confidential and intended solely and for the attention and use of
> the named addressee(s). It may not be disclosed to any other person
> without the express authority of the HPA, or the intended
> recipient, or both. If you are not the intended recipient, you must
> not disclose, copy, distribute or retain this message or any part
> of it. This footnote also confirms that this EMail has been swept
> for computer viruses, but please re-sweep any attachments before
> opening or saving. HTTP://www.HPA.org.uk
> **
> 
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Re: [galaxy-dev] Toolshed initial upload errors

[Paul-Michael Agapow]

[For those who came in late - I've installed a local toolshed, which allows me 
to create repositories, but every time  I attempt to upload files, it errors 
out with "TypeError: array item must be char". For those who come after me, 
here's what I worked out thus far.]

Greg asked:

> Since you've tried uploading various files with no success, the problem is 
> likely
> to be caused by something specific to your environment - possibly the version 
> of
> the mercurial package you're using.  What version of Python are you running, 
> and
> what version of the mercurial package do you have installed with it?  Also, 
> what
> version of Galaxy do you have, and what database / version are you using?

We're CentOS, an older flavour (4), but my Mercurial is up to data (2.1.2). 
Python 2.6.4, Galaxy is 6799:40f1816d6857 (grabbed it fresh last week for 
testing), running it with sqlite. However, the Mercurial is actually installed 
local to the account I'm using, so I wonder if the toolshed is getting confused 
with another version, although hg doesn't seem to be installed on the system.

Further investigations reveal that the files appear to be in the repo 
(database/community_files). The error manifest in the middle of Mercurial, in 
manifest.py where it attempts to coerce a Unicode string into a character 
array. (As there are some reported issues of Windows file names with Unicode 
under Mercurial, and I'm uploading from a Windows machine, I used a Mac to 
create a repo and add a file. Nope, same behaviour.) The Cistrome galaxy fork 
(https://bitbucket.org/cistrome/cistrome-harvard/src/e7e2fdd74496/lib/galaxy/webapps/community/controllers/upload.py)
 mentions occasional similar errors.

I check the Mercurial installation:

% hg --version
Mercurial Distributed SCM (version 2.1.2+10-4d875bb546dc)
...
% hg debuginstall
Checking encoding (UTF-8)...
Checking installed modules 
(/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial)...
Checking templates 
(/home/f0/paul/Installed/lib/python2.6/site-packages/mercurial/templates)...
Checking commit editor...
Checking username...
No problems detected

(Actually, I was missing a username and a user ~/.hgrc file. But making that, 
it passes. Error still persists.)

Work continues.


Paul Agapow (paul-michael.aga...@hpa.org.uk)
Bioinformatics, Health Protection Agency

-
**
The information contained in the EMail and any attachments is
confidential and intended solely and for the attention and use of
the named addressee(s). It may not be disclosed to any other person
without the express authority of the HPA, or the intended
recipient, or both. If you are not the intended recipient, you must
not disclose, copy, distribute or retain this message or any part
of it. This footnote also confirms that this EMail has been swept
for computer viruses, but please re-sweep any attachments before
opening or saving. HTTP://www.HPA.org.uk
**

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Re: [galaxy-dev] Toolshed tribulations--certain types seem unsupported

[Michael Moore]

No joy.  I cannot even find acknowledgement that galaxy is loading any of
my tools or of those in the directory that follows.  The tool is called
analyze_reads and "cat paster.log| grep analyze_r| less produces an end of
file.  The last tool load showing is vcf_tools_extract, but all beyond that
also load and are usable in workflows EXCEPT analyze_reads when any
parameter is specified type="float" or type="integer".  The tools I am
using to edit the files are set for UTF-8 encoding but are not in fact
capable of sending anything but plain old ASCII.  (the very basic vi as my
X isn't working at the moment).

Still examining paster.log was an education.  I am pleased that it got by
many reported errors and still picked up my scan_reads tool.

I guess my next act is to run siege and see if all the instances are
actually responding

Thank you much for the suggestion.  I really needed to see paster.log.

On Mon, Apr 9, 2012 at 3:28 PM, Ross  wrote:

> Michael,
>
> First thing I'd do would be to check paster.log after trying to load
> your new tool and I'll bet there's an 8 bit character or something in
> your text somewhere that causes the tool parser to barf - the error in
> paster.log will tell you the line and character where loading stopped?
>
> On Mon, Apr 9, 2012 at 6:24 PM, Michael Moore
>  wrote:
> > I am testing galaxy for wide use, and I have legacy text files that call
> > algorithms, sorts, and displays.  One such has a tool.xml file with 10
> > parameters, one select, three integer, and one float, with the rest text
> for
> > the moment.  (some will be type="data" later if the runs equate to the
> runs
> > we do outside galaxy)
> >
> > The tool does not show up.  Firefox, emacs and vim all agree that it is
> > well-formed, and galaxy has been properly bounced.  I experimented with
> > removing parameters and found with 7 parameters, I did not have the
> problem,
> > then I noticed that all of them had been changed to text or select in my
> > desperation to make it show up for placement on the workflow.  I
> returned to
> > 10 parameters, but this time all type="select" and type="text", and
> > everything worked.  But slipping even one integer, even with the
> (optional)
> > min max and default tags, and the tool would disappear on restart.
> >
> > Am I looking at a bug, or is there something I need to be doing to make
> this
> > tool visible with numeric parameters?
> >
> > MGM
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>
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