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)
â 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" <g...@bx.psu.edu <mailto:g...@bx.psu.edu>>
Datum: 14-jun.-2013 16:15
Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local
toolshed
Aan: "Joachim Jacob" <joachim.ja...@gmail.com
<mailto:joachim.ja...@gmail.com>>
Cc: <galaxy-...@bx.psu.edu <mailto:galaxy-...@bx.psu.edu>>
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
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