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

[Joachim Jacob | VIB |]

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


On 09/30/2013 02:15 PM, Greg Von Kuster wrote:

Hello Joachim,

What version of Galaxy / Tool Shed code are you using?

[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7



On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB |  wrote:


Hi Greg,


Sorry to dig up this unsolved thread from a few months back.

Recap of the bug: I have developed a small tool. I have put it in my local 
Toolshed, and installed it. After applying some changes to the tool, I 'hg 
push'ed the changes to my repository on my toolshed. I uninstalled the tool, 
and reinstalled it. Since I work with job handlers, I have to restart Galaxy. 
Since I had about ~4 committed changes, I have repeated these steps about 4 
times.


What process do you use for "applying some changes to the tool"?  Do you make 
these changes in a separate development repository and push them to your repository in 
your tool shed?  Or are you making changes to the installed repository in your Galaxy 
instance and attempting to push them back to the repository in your Tool Shed?

First I develop an XML, README, and tool_dependencies.xml in a 
development directory. When finished, I put them in a tool shed repo, by 
uploading a tar ball of these files. I clone the tool shed repo, and 
delete my development directory.  I adjust files in that cloned tool 
shed repo (e.g. fixing typos, adding help,...) and push them back to the 
tool shed repo.


Now, I did some changes to the tool_dependencies.xml and pushed them 
back to the tool shed. Next I update or remove/reinstall the tool via 
the Admin menu. I try to install the dependencies.


That's how I work. I have a feeling that I know what's coming next. :-)


The bug: the tool appears multiple times in the tool management window. 2 times 
as new, and 1 time as uninstalled (since I uninstalled it). The tool is still 
available in the toolbox, although it should not. The 2 installed tools have an 
option 'install', but when I click this I get an internal server error 500.

Galaxy version:
*
[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed repository 
installed into Galaxy.
*

As per your request: the web log of this internal server error.


193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
 HTTP/1.1" 500 - "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0 
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 
Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


When you point your browser to the above "Debug URL", what is the stack trace 
that is displayed?
URL: 
http://galaxy.bits.vib.be/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
File 
'/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', 
line 364 in respond

  app_iter = self.application(environ, detect_start_response)
File 
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', 
line 84 in __call__

  return self.application(environ, start_response)
File 
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', 
line 633 in __call__

  return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
132 in __call__

  return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
190 in handle_request

  body = method( trans, **kwargs )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
line 221 in decorator

  return func( self, trans, *args, **kwargs )
File 
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', 
line 840 in prepare_for_install

  raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
File '/home/galaxy/galaxy-dist/lib/tool_shed/util/common_util.py', line 
110 in tool_shed_get

  response = urlopener.open( uri )
File '/usr/lib64/python2.6/urllib2.py', line 397 in open
  response = meth(req, response)
File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response
  'http', request, response, code, msg, hdrs)
File '/usr/lib64/python2.6/urllib2.py', line 435 in error
  return self._call_chain(*args)
File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain
  result = func(*args)
File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default
  raise HTTPError(req

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

[Joachim Jacob | VIB |]

See attachment.

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


On 09/30/2013 02:15 PM, Peter Cock wrote:

On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
 wrote:

Hi Greg,


Sorry to dig up this unsolved thread from a few months back.

Recap of the bug: I have developed a small tool. I have put it in my local
Toolshed, and installed it. After applying some changes to the tool, I 'hg
push'ed the changes to my repository on my toolshed. I uninstalled the tool,
and reinstalled it. Since I work with job handlers, I have to restart
Galaxy. Since I had about ~4 committed changes, I have repeated these steps
about 4 times.

The bug: the tool appears multiple times in the tool management window. 2
times as new, and 1 time as uninstalled (since I uninstalled it). The tool
is still available in the toolbox, although it should not. The 2 installed
tools have an option 'install', but when I click this I get an internal
server error 500.

Galaxy version:
*
[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
*

As per your request: the web log of this internal server error.


193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
HTTP/1.1" 500 -
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0
(X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu
Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


The postgres database shows:


galaxydb=>  select id, tool_shed, name, owner,
installed_changeset_revision, status, error_message from
tool_shed_repository where name = 'transpose';
  id |  tool_shed   |   name|  owner  |
installed_changeset_revision |   status| error_message
+--+---+-+--+-+---
  45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
| Uninstalled |
  44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
| New |
  43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
| New |
(3 rows)

How should I proceed ?


This is the second time I experience this. On a last note: I have noted also
that I managed to get a repository with different branches in this tool shed
repository, by mixing 'hg push' and uploading a tarball. There seems no easy
way to fixing this.


Kind regards,
Joachim

Hmm - do these "New" entries show up in white on the
"Manage installed tool shed repositories" admin page?

It sounds like a case of what was nicknamed "white ghosts",
some causes of which have been fixed - but I don't think there
was any automated removal of old "white ghosts" (I still have
two on my test system).

Peter




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

[Greg Von Kuster]

Hello Joachim,

What version of Galaxy / Tool Shed code are you using?  

On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB |  wrote:

> Hi Greg,
> 
> 
> Sorry to dig up this unsolved thread from a few months back.
> 
> Recap of the bug: I have developed a small tool. I have put it in my local 
> Toolshed, and installed it. After applying some changes to the tool, I 'hg 
> push'ed the changes to my repository on my toolshed. I uninstalled the tool, 
> and reinstalled it. Since I work with job handlers, I have to restart Galaxy. 
> Since I had about ~4 committed changes, I have repeated these steps about 4 
> times.
> 
What process do you use for "applying some changes to the tool"?  Do you make 
these changes in a separate development repository and push them to your 
repository in your tool shed?  Or are you making changes to the installed 
repository in your Galaxy instance and attempting to push them back to the 
repository in your Tool Shed?


> The bug: the tool appears multiple times in the tool management window. 2 
> times as new, and 1 time as uninstalled (since I uninstalled it). The tool is 
> still available in the toolbox, although it should not. The 2 installed tools 
> have an option 'install', but when I click this I get an internal server 
> error 500.
> 
> Galaxy version:
> *
> [galaxy@galaxy galaxy-dist]$ hg tip
> changeset:   10411:c42567f43aa7
> tag: tip
> user:greg
> date:Mon Aug 19 13:19:56 2013 -0400
> summary: Filter invalid objects when generating the list of 
> repository_dependencies objects that are associated with a tool shed 
> repository installed into Galaxy.
> *
> 
> As per your request: the web log of this internal server error.
> 
> 
> 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET 
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
>  HTTP/1.1" 500 - 
> "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0 
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu 
> Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
> Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


When you point your browser to the above "Debug URL", what is the stack trace 
that is displayed?


> 
> 
> The postgres database shows:
> 
> 
> galaxydb=>  select id, tool_shed, name, owner, 
> installed_changeset_revision, status, error_message from tool_shed_repository 
> where name = 'transpose';
> id |  tool_shed   |   name|  owner  | 
> installed_changeset_revision |   status| error_message
> +--+---+-+--+-+---
> 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
>  | Uninstalled |
> 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
>  | New |
> 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
>  | New |
> (3 rows)
> 


These repositories in the "New" state look like the so-called "white ghosts" 
that cropped up for a time.  The issues that resulted in their creation have 
been resolved, but some of the fixes will not be available in the distribution 
until the next Galaxy release, which is not yet scheduled.


> How should I proceed ?

You'll undoubtedly need to manually fix your database with sql - delete these 
records in the "New" state and all associated recoirds defined by foreign keys.


> 
> 
> This is the second time I experience this. On a last note: I have noted also 
> that I managed to get a repository with different branches in this tool shed 
> repository, by mixing 'hg push' and uploading a tarball. There seems no easy 
> way to fixing this.
> 
> 
> Kind regards,
> Joachim
> 
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
> On 06/14/2013 04:15 PM, Greg Von Kuster wrote:
>> 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
>> 
>> 
>> On Jun 14, 2013, at 3:41 AM, Joachim Jacob > > 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 

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

[Peter Cock]

On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB |
 wrote:
> Hi Greg,
>
>
> Sorry to dig up this unsolved thread from a few months back.
>
> Recap of the bug: I have developed a small tool. I have put it in my local
> Toolshed, and installed it. After applying some changes to the tool, I 'hg
> push'ed the changes to my repository on my toolshed. I uninstalled the tool,
> and reinstalled it. Since I work with job handlers, I have to restart
> Galaxy. Since I had about ~4 committed changes, I have repeated these steps
> about 4 times.
>
> The bug: the tool appears multiple times in the tool management window. 2
> times as new, and 1 time as uninstalled (since I uninstalled it). The tool
> is still available in the toolbox, although it should not. The 2 installed
> tools have an option 'install', but when I click this I get an internal
> server error 500.
>
> Galaxy version:
> *
> [galaxy@galaxy galaxy-dist]$ hg tip
> changeset:   10411:c42567f43aa7
> tag: tip
> user:greg
> date:Mon Aug 19 13:19:56 2013 -0400
> summary: Filter invalid objects when generating the list of
> repository_dependencies objects that are associated with a tool shed
> repository installed into Galaxy.
> *
>
> As per your request: the web log of this internal server error.
>
> 
> 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3
> HTTP/1.1" 500 -
> "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0
> (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu
> Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"
> Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486
> 
>
> The postgres database shows:
>
> 
> galaxydb=>  select id, tool_shed, name, owner,
> installed_changeset_revision, status, error_message from
> tool_shed_repository where name = 'transpose';
>  id |  tool_shed   |   name|  owner  |
> installed_changeset_revision |   status| error_message
> +--+---+-+--+-+---
>  45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1
> | Uninstalled |
>  44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303
> | New |
>  43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3
> | New |
> (3 rows)
> 
> How should I proceed ?
>
>
> This is the second time I experience this. On a last note: I have noted also
> that I managed to get a repository with different branches in this tool shed
> repository, by mixing 'hg push' and uploading a tarball. There seems no easy
> way to fixing this.
>
>
> Kind regards,
> Joachim

Hmm - do these "New" entries show up in white on the
"Manage installed tool shed repositories" admin page?

It sounds like a case of what was nicknamed "white ghosts",
some causes of which have been fixed - but I don't think there
was any automated removal of old "white ghosts" (I still have
two on my test system).

Peter
___
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] Messed up a tool installation from a local toolshed

[Joachim Jacob | VIB |]

Hi Greg,


Sorry to dig up this unsolved thread from a few months back.

Recap of the bug: I have developed a small tool. I have put it in my 
local Toolshed, and installed it. After applying some changes to the 
tool, I 'hg push'ed the changes to my repository on my toolshed. I 
uninstalled the tool, and reinstalled it. Since I work with job 
handlers, I have to restart Galaxy. Since I had about ~4 committed 
changes, I have repeated these steps about 4 times.


The bug: the tool appears multiple times in the tool management window. 
2 times as new, and 1 time as uninstalled (since I uninstalled it). The 
tool is still available in the toolbox, although it should not. The 2 
installed tools have an option 'install', but when I click this I get an 
internal server error 500.


Galaxy version:
*
[galaxy@galaxy galaxy-dist]$ hg tip
changeset:   10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of 
repository_dependencies objects that are associated with a tool shed 
repository installed into Galaxy.

*

As per your request: the web log of this internal server error.


193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3 
HTTP/1.1" 500 - 
"http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; 
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) 
Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36"

Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486


The postgres database shows:


galaxydb=>  select id, tool_shed, name, owner, 
installed_changeset_revision, status, error_message from 
tool_shed_repository where name = 'transpose';
 id |  tool_shed   |   name|  owner  | 
installed_changeset_revision |   status| error_message

+--+---+-+--+-+---
 45 | toolshed.bits.vib.be | transpose | joachim | 
cee0157acee1 | Uninstalled |
 44 | toolshed.bits.vib.be | transpose | joachim | 
2fa0462b9303 | New |
 43 | toolshed.bits.vib.be | transpose | joachim | 
e08a6d9e97a3 | New |

(3 rows)

How should I proceed ?


This is the second time I experience this. On a last note: I have noted 
also that I managed to get a repository with different branches in this 
tool shed repository, by mixing 'hg push' and uploading a tarball. There 
seems no easy way to fixing this.



Kind regards,
Joachim

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


On 06/14/2013 04:15 PM, Greg Von Kuster wrote:

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


On Jun 14, 2013, at 3:41 AM, Joachim Jacob > 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' (...). But 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_reques

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

[Greg Von Kuster]

 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" 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" >> <mailto:joachim.ja...@gmail.com>>
>>> Cc: 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

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

[Greg Von Kuster]

u | 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" 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"  <mailto:joachim.ja...@gmail.com>>
> Cc: 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
>> 
> 
> ___
> 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] Messed up a tool installation from a local toolshed

[Joachim Jacob | VIB |]

stalled |

*

Thanks,

Joachim Jacob



Van: "Greg Von Kuster" 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" <mailto:joachim.ja...@gmail.com>>

Cc: 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



___
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/

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

[Greg Von Kuster]

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


On Jun 14, 2013, at 3:41 AM, Joachim Jacob  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' (...). But 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 
> -- 
> @joachimjacob
> ___
> 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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and other Galaxy lists, please use the interface at:
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