Re: [galaxy-dev] Messed up a tool installation from a local toolshed

20 Jun 2013

      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 | <joachim.jacob@vib.be> 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 | <joachim.jacob@vib.be> 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)
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" <greg@bx.psu.edu <mailto:greg@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.jacob@gmail.com <mailto:joachim.jacob@gmail.com>>
Cc: <galaxy-dev@bx.psu.edu <mailto:galaxy-dev@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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Greg Von Kuster

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