Messed up a tool installation from a local toolshed

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Messed up a tool installation from a local toolshed

Joachim Jacob
Hi all,

I have developed a tool in our local Galaxy, and imported it in a local
toolshed. I next removed the 'dev' version of the tool in Galaxy, and
installed it now via het Tool Shed Manager.

I got an error that the dependencies could not be installed. If figured
it out that it (needed to add an extra shell_command in the
tool_dependencies) (and the mount point on my system needs to have exec
permissions of course).

So I updated the tool in the toolshed. BUT, then I uninstalled the tool
from Galaxy, and reinstalled it from the Tool Shed ... instead of just
updating. Anyway, it has happened.

Now I have the tool listed in my 'Install Tool Shed Repositories', and
when I click on it, it says 'this tool is not installed'. The only
action I can apply on this installed tool shed repository is 'Install'.
Clicking on that 'install' button, leads me to an error page (http error
500).

******************************
URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
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:221 in decorator          view
 >>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
prepare_for_install          view
 >>  raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
Module tool_shed.util.common_util:110 in tool_shed_get          view
 >>  response = urlopener.open( uri )
Module urllib2:397 in open          view
 >>  response = meth(req, response)
Module urllib2:510 in http_response          view
 >>  'http', request, response, code, msg, hdrs)
Module urllib2:435 in error          view
 >>  return self._call_chain(*args)
Module urllib2:369 in _call_chain          view
 >>  result = func(*args)
Module urllib2:518 in http_error_default          view
 >>  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
************************************

The same happens when I go to the Tool Shed, and try to install the tool
from there: Galaxy detects that the tool has been installed before, and
points me to that 500 error page.

Any help is heartily appreciated,

Thanks,
Joachim

--
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


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Re: Messed up a tool installation from a local toolshed

Joachim Jacob
Hi Greg,

Thanks, and sorry for the long delay in response.

To make the problem clear:
https://dl.dropboxusercontent.com/u/18352887/GalaxyToolShedToolError.ogv

The version of our Galaxy is:
*****************************
[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9944:cea3ddf6cdda tip
Update tag for stable_2013.06.03
branch: stable
commit: 6 modified, 284 unknown
update: (current)
*****************************

The logs on the 500 error page is:
*****************************
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ HTTPError: HTTP Error 500: Internal Server Error
URL:
http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
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:221 in decorator view
 >> return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
prepare_for_install view
 >> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
Module tool_shed.util.common_util:110 in tool_shed_get view
 >> response = urlopener.open( uri )
Module urllib2:397 in open view
 >> response = meth(req, response)
Module urllib2:510 in http_response view
 >> 'http', request, response, code, msg, hdrs)
Module urllib2:435 in error view
 >> return self._call_chain(*args)
Module urllib2:369 in _call_chain view
 >> result = func(*args)
Module urllib2:518 in http_error_default view
 >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
*****************************

In the galaxy database, the tool_shed_repository table shows:

********************************
galaxydb=> select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from
tool_shed_repository;
id | tool_shed | name | owner | installed_changeset_revision | status |
error_message
----+------------------------+----------------------------+---------------+------------------------------+-------------+---------------
4 | toolshed.g2.bx.psu.edu | freebayes | devteam | 213a3d6b579a |
Installed |
2 | 192.168.10.23:9009 | glinechart | joachim | 75ef0fbe189a | Installed |
8 | toolshed.g2.bx.psu.edu | bedtools | aaronquinlan | 41bba3e648d1 |
Installed |
1 | 192.168.10.24:9009 | quarc_read_quality_control | joachim |
fa5ddf4118c0 | Uninstalled |
6 | 192.168.10.23:9009 | fastqseqlen | joachim | 3f22736718ef | Installed |
3 | 192.168.10.23:9009 | quarc_bq | joachim | 4dbdbb424a67 | Installed |
15 | 192.168.10.23:9009 | qualimap_suite | joachim | 8c7e29fa58b5 |
Installed |
7 | toolshed.g2.bx.psu.edu | bwa_wrappers | devteam | ffa8aaa14f7c |
Installed |
9 | toolshed.g2.bx.psu.edu | picard | devteam | e0232cbac965 | Installed |
11 | toolshed.g2.bx.psu.edu | bowtie_color_wrappers | devteam |
fd0914e451c5 | Installed |
12 | toolshed.g2.bx.psu.edu | lastz | devteam | 0801f8207d30 | Installed |
20 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | 62a1de8c8aae |
Installed |
21 | toolshed.g2.bx.psu.edu | emboss_datatypes | devteam | a89163f31369
| Installed |
23 | toolshed.g2.bx.psu.edu | trinityrnaseq | bhaas | 177bb1b443db |
Installed |
14 | toolshed.g2.bx.psu.edu | fastq_mcf | jjohnson | 217aedbdd0d0 |
Installed |
22 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | b45f604a08ac |
Installed |
5 | toolshed.g2.bx.psu.edu | deseq_and_sam2counts | nikhil-joshi |
3348f484c49c | Installed |
18 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 93911bac43da | Installed |
19 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | f320093f1e8e |
Deactivated |
17 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 6adc485b6dc0 |
Uninstalled |
10 | toolshed.g2.bx.psu.edu | bowtie_wrappers | devteam | 0c7e4eadfb3c |
Installed |
16 | toolshed.g2.bx.psu.edu | cummerbund | jjohnson | ebb9a992508d |
Installed |
24 | toolshed.g2.bx.psu.edu | seq_select_by_id | peterjc | 28d52478ace9
| Installed |
13 | toolshed.g2.bx.psu.edu | lastz_paired_reads | devteam |
96825cee5c25 | Installed |
25 | toolshed.g2.bx.psu.edu | muscle | edward-kirton | 38a28f5f9449 |
Installed |
26 | localhost:9009 | hmmer | joachim | fc2339abcab7 | New |
27 | localhost:9009 | hmmer | joachim | d724499758f9 | Uninstalled |
28 | localhost:9009 | blat | joachim | e2b0a830c892 | Installed |
29 | toolshed.g2.bx.psu.edu | prop_venn | idot | cc6707a1e044 |
Uninstalled |
*****************************

Thanks,

Joachim Jacob



Van: "Greg Von Kuster" <[hidden email] <mailto:[hidden email]>>
Datum: 14-jun.-2013 16:15
Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local
toolshed
Aan: "Joachim Jacob" <[hidden email]
<mailto:[hidden email]>>
Cc: <[hidden email] <mailto:[hidden email]>>

Hello Joachim,

What version of Galaxy are your running?

What does the tool shed paster go show for the 500 Internal Server Error?

Also, run the following sql manually in your Galaxy database and send
the results.

select id, tool_shed, name, owner, installed_changeset_revision, status,
error_message from tool_shed_repository;

Thanks,

Greg Von Kuster

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote:

> Hi all,
>
> I have developed a tool in our local Galaxy, and imported it in a
> local toolshed. I next removed the 'dev' version of the tool in
> Galaxy, and installed it now via het Tool Shed Manager.
>
> I got an error that the dependencies could not be installed. If
> figured it out that it (needed to add an extra shell_command in the
> tool_dependencies) (and the mount point on my system needs to have
> exec permissions of course).
>
> So I updated the tool in the toolshed. BUT, then I uninstalled the
> tool from Galaxy, and reinstalled it from the Tool Shed ... instead of
> just updating. Anyway, it has happened.
>
> Now I have the tool listed in my 'Install Tool Shed Repositories', and
> when I click on it, it says 'this tool is not installed'. The only
> action I can apply on this installed tool shed repository is
> 'Install'. Clicking on that 'install' button, leads me to an error
> page (http error 500).
>
> ******************************
> URL:
> http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
> 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:221 in decorator view
> >> return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in
> prepare_for_install view
> >> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
> Module tool_shed.util.common_util:110 in tool_shed_get view
> >> response = urlopener.open( uri )
> Module urllib2:397 in open view
> >> response = meth(req, response)
> Module urllib2:510 in http_response view
> >> 'http', request, response, code, msg, hdrs)
> Module urllib2:435 in error view
> >> return self._call_chain(*args)
> Module urllib2:369 in _call_chain view
> >> result = func(*args)
> Module urllib2:518 in http_error_default view
> >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
> HTTPError: HTTP Error 500: Internal Server Error
> ************************************
>
> The same happens when I go to the Tool Shed, and try to install the
> tool from there: Galaxy detects that the tool has been installed
> before, and points me to that 500 error page.
>
> Any help is heartily appreciated,
>
> Thanks,
> Joachim
>

___________________________________________________________
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: Messed up a tool installation from a local toolshed

Greg Von Kuster
Hello Joachim,

What version of Galaxy are you running?

It looks like the 500 error should be displayed in your tool shed's paster log.

Thanks,

Greg Von Kuster


On Jun 19, 2013, at 2:46 AM, Joachim Jacob | VIB | <[hidden email]> wrote:

> Hi Greg,
>
> Thanks, and sorry for the long delay in response.
>
> To make the problem clear: https://dl.dropboxusercontent.com/u/18352887/GalaxyToolShedToolError.ogv
>
> The version of our Galaxy is:
> *****************************
> [galaxy@galaxy galaxy-dist]$ hg summary
> parent: 9944:cea3ddf6cdda tip
> Update tag for stable_2013.06.03
> branch: stable
> commit: 6 modified, 284 unknown
> update: (current)
> *****************************
>
> The logs on the 500 error page is:
> *****************************
> Error Traceback:
> View as: Interactive | Text | XML (full)
> ⇝ HTTPError: HTTP Error 500: Internal Server Error
> URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
> 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:221 in decorator view
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view
>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
> Module tool_shed.util.common_util:110 in tool_shed_get view
>>> response = urlopener.open( uri )
> Module urllib2:397 in open view
>>> response = meth(req, response)
> Module urllib2:510 in http_response view
>>> 'http', request, response, code, msg, hdrs)
> Module urllib2:435 in error view
>>> return self._call_chain(*args)
> Module urllib2:369 in _call_chain view
>>> result = func(*args)
> Module urllib2:518 in http_error_default view
>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
> HTTPError: HTTP Error 500: Internal Server Error
> *****************************
>
> In the galaxy database, the tool_shed_repository table shows:
>
> ********************************
> galaxydb=> select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository;
> id | tool_shed | name | owner | installed_changeset_revision | status | error_message
> ----+------------------------+----------------------------+---------------+------------------------------+-------------+---------------
> 4 | toolshed.g2.bx.psu.edu | freebayes | devteam | 213a3d6b579a | Installed |
> 2 | 192.168.10.23:9009 | glinechart | joachim | 75ef0fbe189a | Installed |
> 8 | toolshed.g2.bx.psu.edu | bedtools | aaronquinlan | 41bba3e648d1 | Installed |
> 1 | 192.168.10.24:9009 | quarc_read_quality_control | joachim | fa5ddf4118c0 | Uninstalled |
> 6 | 192.168.10.23:9009 | fastqseqlen | joachim | 3f22736718ef | Installed |
> 3 | 192.168.10.23:9009 | quarc_bq | joachim | 4dbdbb424a67 | Installed |
> 15 | 192.168.10.23:9009 | qualimap_suite | joachim | 8c7e29fa58b5 | Installed |
> 7 | toolshed.g2.bx.psu.edu | bwa_wrappers | devteam | ffa8aaa14f7c | Installed |
> 9 | toolshed.g2.bx.psu.edu | picard | devteam | e0232cbac965 | Installed |
> 11 | toolshed.g2.bx.psu.edu | bowtie_color_wrappers | devteam | fd0914e451c5 | Installed |
> 12 | toolshed.g2.bx.psu.edu | lastz | devteam | 0801f8207d30 | Installed |
> 20 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | 62a1de8c8aae | Installed |
> 21 | toolshed.g2.bx.psu.edu | emboss_datatypes | devteam | a89163f31369 | Installed |
> 23 | toolshed.g2.bx.psu.edu | trinityrnaseq | bhaas | 177bb1b443db | Installed |
> 14 | toolshed.g2.bx.psu.edu | fastq_mcf | jjohnson | 217aedbdd0d0 | Installed |
> 22 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | b45f604a08ac | Installed |
> 5 | toolshed.g2.bx.psu.edu | deseq_and_sam2counts | nikhil-joshi | 3348f484c49c | Installed |
> 18 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 93911bac43da | Installed |
> 19 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | f320093f1e8e | Deactivated |
> 17 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 6adc485b6dc0 | Uninstalled |
> 10 | toolshed.g2.bx.psu.edu | bowtie_wrappers | devteam | 0c7e4eadfb3c | Installed |
> 16 | toolshed.g2.bx.psu.edu | cummerbund | jjohnson | ebb9a992508d | Installed |
> 24 | toolshed.g2.bx.psu.edu | seq_select_by_id | peterjc | 28d52478ace9 | Installed |
> 13 | toolshed.g2.bx.psu.edu | lastz_paired_reads | devteam | 96825cee5c25 | Installed |
> 25 | toolshed.g2.bx.psu.edu | muscle | edward-kirton | 38a28f5f9449 | Installed |
> 26 | localhost:9009 | hmmer | joachim | fc2339abcab7 | New |
> 27 | localhost:9009 | hmmer | joachim | d724499758f9 | Uninstalled |
> 28 | localhost:9009 | blat | joachim | e2b0a830c892 | Installed |
> 29 | toolshed.g2.bx.psu.edu | prop_venn | idot | cc6707a1e044 | Uninstalled |
> *****************************
>
> Thanks,
>
> Joachim Jacob
>
>
>
> Van: "Greg Von Kuster" <[hidden email] <mailto:[hidden email]>>
> Datum: 14-jun.-2013 16:15
> Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local toolshed
> Aan: "Joachim Jacob" <[hidden email] <mailto:[hidden email]>>
> Cc: <[hidden email] <mailto:[hidden email]>>
>
> Hello Joachim,
>
> What version of Galaxy are your running?
>
> What does the tool shed paster go show for the 500 Internal Server Error?
>
> Also, run the following sql manually in your Galaxy database and send the results.
>
> select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository;
>
> Thanks,
>
> Greg Von Kuster
>
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
>
>
> On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote:
>> Hi all,
>>
>> I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager.
>>
>> I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course).
>>
>> So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened.
>>
>> Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500).
>>
>> ******************************
>> URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
>> 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:221 in decorator view
>>>> return func( self, trans, *args, **kwargs )
>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view
>>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
>> Module tool_shed.util.common_util:110 in tool_shed_get view
>>>> response = urlopener.open( uri )
>> Module urllib2:397 in open view
>>>> response = meth(req, response)
>> Module urllib2:510 in http_response view
>>>> 'http', request, response, code, msg, hdrs)
>> Module urllib2:435 in error view
>>>> return self._call_chain(*args)
>> Module urllib2:369 in _call_chain view
>>>> result = func(*args)
>> Module urllib2:518 in http_error_default view
>>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
>> HTTPError: HTTP Error 500: Internal Server Error
>> ************************************
>>
>> The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page.
>>
>> Any help is heartily appreciated,
>>
>> Thanks,
>> Joachim
>>
>
> ___________________________________________________________
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Open this post in threaded view
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Re: Messed up a tool installation from a local toolshed

Greg Von Kuster
Hello Joachim,

It looks like you have an invalid URL you are attempting to us for your top shed (this looks to me like your Galaxy paster log, not your tool shed paster log).  Is your tool shed running at 'http://localhost:9009/, or some other port?

Also, when this error occurs, you can point your browser to the link displayed in the log where it states "Debug at: http://localhost/_debug/view/1371632354", and it should display a traceback which should help determine issues like this.

Greg Von Kuster


On Jun 20, 2013, at 4:39 AM, Joachim Jacob | VIB | <[hidden email]> wrote:

> Hello Greg,
>
> The version of Galaxy:
> arent: 9944:cea3ddf6cdda tip
> Update tag for stable_2013.06.03
> branch: stable
>
> Sorry, forgot to paste the web.log:
> *****************************
> tool_shed.tool_shed_registry DEBUG 2013-06-20 10:35:45,718 Invalid url 'http://localhost:9009/' received by tool shed registry's password_manager_for_url method.
> ::1 - - [20/Jun/2013:10:35:45 +0200] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7 HTTP/1.1" 500 - "http://localhost/admin_toolshed/browse_repositories" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31"
> Debug at: http://localhost/_debug/view/1371632354
> *****************************
>
> Cheers,
> Joachim
>
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
>
>
> On 06/20/2013 01:07 AM, Greg Von Kuster wrote:
>> Hello Joachim,
>>
>> What version of Galaxy are you running?
>>
>> It looks like the 500 error should be displayed in your tool shed's paster log.
>>
>> Thanks,
>>
>> Greg Von Kuster
>>
>>
>> On Jun 19, 2013, at 2:46 AM, Joachim Jacob | VIB | <[hidden email]> wrote:
>>
>>> Hi Greg,
>>>
>>> Thanks, and sorry for the long delay in response.
>>>
>>> To make the problem clear: https://dl.dropboxusercontent.com/u/18352887/GalaxyToolShedToolError.ogv
>>>
>>> The version of our Galaxy is:
>>> *****************************
>>> [galaxy@galaxy galaxy-dist]$ hg summary
>>> parent: 9944:cea3ddf6cdda tip
>>> Update tag for stable_2013.06.03
>>> branch: stable
>>> commit: 6 modified, 284 unknown
>>> update: (current)
>>> *****************************
>>>
>>> The logs on the 500 error page is:
>>> *****************************
>>> Error Traceback:
>>> View as: Interactive | Text | XML (full)
>>> ⇝ HTTPError: HTTP Error 500: Internal Server Error
>>> URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
>>> 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:221 in decorator view
>>>>> return func( self, trans, *args, **kwargs )
>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view
>>>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
>>> Module tool_shed.util.common_util:110 in tool_shed_get view
>>>>> response = urlopener.open( uri )
>>> Module urllib2:397 in open view
>>>>> response = meth(req, response)
>>> Module urllib2:510 in http_response view
>>>>> 'http', request, response, code, msg, hdrs)
>>> Module urllib2:435 in error view
>>>>> return self._call_chain(*args)
>>> Module urllib2:369 in _call_chain view
>>>>> result = func(*args)
>>> Module urllib2:518 in http_error_default view
>>>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
>>> HTTPError: HTTP Error 500: Internal Server Error
>>> *****************************
>>>
>>> In the galaxy database, the tool_shed_repository table shows:
>>>
>>> ********************************
>>> galaxydb=> select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository;
>>> id | tool_shed | name | owner | installed_changeset_revision | status | error_message
>>> ----+------------------------+----------------------------+---------------+------------------------------+-------------+---------------
>>> 4 | toolshed.g2.bx.psu.edu | freebayes | devteam | 213a3d6b579a | Installed |
>>> 2 | 192.168.10.23:9009 | glinechart | joachim | 75ef0fbe189a | Installed |
>>> 8 | toolshed.g2.bx.psu.edu | bedtools | aaronquinlan | 41bba3e648d1 | Installed |
>>> 1 | 192.168.10.24:9009 | quarc_read_quality_control | joachim | fa5ddf4118c0 | Uninstalled |
>>> 6 | 192.168.10.23:9009 | fastqseqlen | joachim | 3f22736718ef | Installed |
>>> 3 | 192.168.10.23:9009 | quarc_bq | joachim | 4dbdbb424a67 | Installed |
>>> 15 | 192.168.10.23:9009 | qualimap_suite | joachim | 8c7e29fa58b5 | Installed |
>>> 7 | toolshed.g2.bx.psu.edu | bwa_wrappers | devteam | ffa8aaa14f7c | Installed |
>>> 9 | toolshed.g2.bx.psu.edu | picard | devteam | e0232cbac965 | Installed |
>>> 11 | toolshed.g2.bx.psu.edu | bowtie_color_wrappers | devteam | fd0914e451c5 | Installed |
>>> 12 | toolshed.g2.bx.psu.edu | lastz | devteam | 0801f8207d30 | Installed |
>>> 20 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | 62a1de8c8aae | Installed |
>>> 21 | toolshed.g2.bx.psu.edu | emboss_datatypes | devteam | a89163f31369 | Installed |
>>> 23 | toolshed.g2.bx.psu.edu | trinityrnaseq | bhaas | 177bb1b443db | Installed |
>>> 14 | toolshed.g2.bx.psu.edu | fastq_mcf | jjohnson | 217aedbdd0d0 | Installed |
>>> 22 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | b45f604a08ac | Installed |
>>> 5 | toolshed.g2.bx.psu.edu | deseq_and_sam2counts | nikhil-joshi | 3348f484c49c | Installed |
>>> 18 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 93911bac43da | Installed |
>>> 19 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | f320093f1e8e | Deactivated |
>>> 17 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 6adc485b6dc0 | Uninstalled |
>>> 10 | toolshed.g2.bx.psu.edu | bowtie_wrappers | devteam | 0c7e4eadfb3c | Installed |
>>> 16 | toolshed.g2.bx.psu.edu | cummerbund | jjohnson | ebb9a992508d | Installed |
>>> 24 | toolshed.g2.bx.psu.edu | seq_select_by_id | peterjc | 28d52478ace9 | Installed |
>>> 13 | toolshed.g2.bx.psu.edu | lastz_paired_reads | devteam | 96825cee5c25 | Installed |
>>> 25 | toolshed.g2.bx.psu.edu | muscle | edward-kirton | 38a28f5f9449 | Installed |
>>> 26 | localhost:9009 | hmmer | joachim | fc2339abcab7 | New |
>>> 27 | localhost:9009 | hmmer | joachim | d724499758f9 | Uninstalled |
>>> 28 | localhost:9009 | blat | joachim | e2b0a830c892 | Installed |
>>> 29 | toolshed.g2.bx.psu.edu | prop_venn | idot | cc6707a1e044 | Uninstalled |
>>> *****************************
>>>
>>> Thanks,
>>>
>>> Joachim Jacob
>>>
>>>
>>>
>>> Van: "Greg Von Kuster" <[hidden email] <mailto:[hidden email]>>
>>> Datum: 14-jun.-2013 16:15
>>> Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local toolshed
>>> Aan: "Joachim Jacob" <[hidden email] <mailto:[hidden email]>>
>>> Cc: <[hidden email] <mailto:[hidden email]>>
>>>
>>> Hello Joachim,
>>>
>>> What version of Galaxy are your running?
>>>
>>> What does the tool shed paster go show for the 500 Internal Server Error?
>>>
>>> Also, run the following sql manually in your Galaxy database and send the results.
>>>
>>> select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository;
>>>
>>> Thanks,
>>>
>>> Greg Von Kuster
>>>
>>> Joachim Jacob
>>> Contact details: http://www.bits.vib.be/index.php/about/80-team
>>>
>>>
>>> On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote:
>>>> Hi all,
>>>>
>>>> I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager.
>>>>
>>>> I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course).
>>>>
>>>> So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened.
>>>>
>>>> Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500).
>>>>
>>>> ******************************
>>>> URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/&repository_ids=84cbaf0b6bf7a1a9&changeset_revisions=fc2339abcab7
>>>> 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:221 in decorator view
>>>>>> return func( self, trans, *args, **kwargs )
>>>> Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view
>>>>>> raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
>>>> Module tool_shed.util.common_util:110 in tool_shed_get view
>>>>>> response = urlopener.open( uri )
>>>> Module urllib2:397 in open view
>>>>>> response = meth(req, response)
>>>> Module urllib2:510 in http_response view
>>>>>> 'http', request, response, code, msg, hdrs)
>>>> Module urllib2:435 in error view
>>>>>> return self._call_chain(*args)
>>>> Module urllib2:369 in _call_chain view
>>>>>> result = func(*args)
>>>> Module urllib2:518 in http_error_default view
>>>>>> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
>>>> HTTPError: HTTP Error 500: Internal Server Error
>>>> ************************************
>>>>
>>>> The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page.
>>>>
>>>> Any help is heartily appreciated,
>>>>
>>>> Thanks,
>>>> Joachim
>>>>
>>> ___________________________________________________________
>>> 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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