Re: [galaxy-dev] History not updating automatically

[Joachim Jacob |VIB|]

Hi,


I have a similar - but not identical issue. The history panel is not 
being updated: I have to restart Galaxy to see the updated panel.
It appears only to happen after an error relating to the history API of 
Galaxy (it's a popup error, and I have closed it).


My apache config (thanks for any hints and tweaks to improve my setup).

[galaxy@galaxy conf.d]$ cat galaxy_web.conf

NameVirtualHost 157.193.230.103:80
VirtualHost 157.193.230.103:80
ServerName galaxy.bits.vib.be

Proxy balancer://galaxy
BalancerMember http://localhost:8080
BalancerMember http://localhost:8081
BalancerMember http://localhost:8082
BalancerMember http://localhost:8083
BalancerMember http://localhost:8084
BalancerMember http://localhost:8085
BalancerMember http://localhost:8086
BalancerMember http://localhost:8087
BalancerMember http://localhost:8088
BalancerMember http://localhost:8089
BalancerMember http://localhost:8090
BalancerMember http://localhost:8091
BalancerMember http://localhost:8092
/Proxy
RewriteEngine on
RewriteLog /tmp/apacheGalaxy.log
### LDAP authentication will be implemented later
# Location /
# AuthType Basic
# AuthBasicProvider ldap
# AuthLDAPURL ldap://smeagol.vib.be:389/DC=vib,DC=local?sAMAccountName
# AuthLDAPBindDN vib\administrator
# AuthLDAPBindPassword tofillin
# AuthzLDAPAuthoritative off
# Require valid-user
# # Set the REMOTE_USER header to the contents of the LDAP query 
response's uid attribute

# RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}
# /Location
RewriteRule ^/static/style/(.*) 
/home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*) 
/home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]

RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) balancer://galaxy$1 [P]
/VirtualHost


Cheers,
Joachim

Joachim Jacob

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

On 01/28/2013 09:02 PM, Langhorst, Brad wrote:

Nate:

I used the config from the wiki directly…
Location /
…
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
...
/Location

but I also had a section like this below it...

#   Location /api
#   Satisfy Any
#   Allow from all
#   /Location

I thought that the /api location would inherit the auth and headers stuff of 
it's container, but that's not true.

Commenting the api location fixes the problem form e.


Brad

On Jan 28, 2013, at 2:35 PM, Nate Coraor n...@bx.psu.edu
  wrote:


Hi Brad and Sajoscha,

Is there any chance that your proxy configurations are not passing the username 
in the REMOTE_USER header when the request is to an /api path?  Could you 
provide the relevant portions of your proxy server configs?

Thanks,
--nate

On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:


Hi Sajoscha:

I have exactly the same problem… it started about a month ago.

Also with external ldap auth.

I have not yet investigated in detail, since it's not crippling - just annoying.

Brad


On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
wrote:


Hi list,

I have a weird problem after updating to the latest version.

After doing the update as usual, the history panel is not updating 
automatically anymore. And when I press refresh, I get an javascript popup 
saying:

Error getting history updates from the server.
Forbidden


Also, in the log I see the following:

galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as '(null)' 
externally, but has a cookie as 'sa...@embl.de' invalidating session


We are using LDAP to connect to Galaxy, but I don't know if this has something 
to do with the problem. As I said, it was working perfectly fine before the 
update.

Does someone know the problem or has any ideas?

Thanks for your help,

Sajoscha



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--
Brad Langhorst
langho...@neb.com






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--
Brad Langhorst
langho...@neb.com






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[galaxy-dev] show urls in csv (in eye mode)

[Hagai Cohen]

Hi,
I have a tool which outputs a csv file with links.
When I press the eye icon - I would like these links to be shown as links
in the browser.
It is possible?

Thanks,
Hagai
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Re: [galaxy-dev] show urls in csv (in eye mode)

[Hagai Cohen]

Hi,
I found a simple solution.

In the file:
templates/dataset/tabular_chunked.mako
inside the method: renderCell - replace all jQuery .text(..) calls with
.html(..) calls.

Note:
Any entry in the csv with html syntax will be shown like html (links, tags.
etc).





On Tue, Jan 29, 2013 at 1:39 PM, Hagai Cohen haga...@gmail.com wrote:

 Hi,
 I have a tool which outputs a csv file with links.
 When I press the eye icon - I would like these links to be shown as links
 in the browser.
 It is possible?

 Thanks,
 Hagai

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[galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

Users are getting the following error when trying to add a tool from the tool 
shed repository on our local galaxy instance.

An error occurred. See the error logs for more information. (Turn debug on to 
display exception reports here)

The galaxy server log shows the message included below. The main error is 
ValueError: too many values to unpack . From a similar previous post, the 
resolution was to use the latest code from Galaxy central. I just ran an hg 
pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but 
we still get the same error.

Any ideas?

(server log)
[29/Jan/2013:08:19:05 -0400] GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
 HTTP/1.1 500 - 
http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919;
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, 
like Gecko) Version/5.1.7 Safari/534.57.2
Error - type 'exceptions.ValueError': too many values to unpack
URL: 
https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
File 
'/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
 line 143 in __call__
  app_iter = self.application(environ, start_response)
File 
'/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
 line 80 in __call__
  return self.application(environ, start_response)
File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
 line 91 in __call__
  return self.app( environ, start_response )
File 
'/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
 line 632 in __call__
  return self.application(environ, start_response)
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', 
line 160 in __call__
  body = method( trans, **kwargs )
File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
line 206 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install
  description, repository_clone_url, changeset_revision, ctx_rev, 
repository_owner, tool_dependencies = repo_info_tuple
ValueError: too many values to unpack


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill

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Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Greg Von Kuster]

Hi Michael,

The previous post you mention is outdated.  The main Galaxy tool shed from 
which you are pulling has been tracking Galaxy dist for some time now, so you 
should only have to update to that.  

However, the communication layer between Galaxy and the tool shed is backward 
compatible to the December 20, 2012 Galaxy release, so whether you have updated 
from Galaxy central or Galaxy dist, you should not be seeing the behavior you 
describe.  

If you do, in fact, track Galaxy central though, and use the main Galaxy tool 
shed, you may experience some strange behavior because the the development code 
may include new features that are not available on the main tool shed since it 
tracks Galaxy dist.

What is the result of typing the following in your Galaxy installation 
directory?

hg heads

Thanks,

Greg Von Kuster


On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote:

 Users are getting the following error when trying to add a tool from the tool 
 shed repository on our local galaxy instance.
 
 An error occurred. See the error logs for more information. (Turn debug on 
 to display exception reports here)
 
 The galaxy server log shows the message included below. The main error is 
 ValueError: too many values to unpack . From a similar previous post, the 
 resolution was to use the latest code from Galaxy central. I just ran an hg 
 pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), 
 but we still get the same error.
 
 Any ideas?
 
 (server log)
 [29/Jan/2013:08:19:05 -0400] GET 
 /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
  HTTP/1.1 500 - 
 http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919;
  Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, 
 like Gecko) Version/5.1.7 Safari/534.57.2
 Error - type 'exceptions.ValueError': too many values to unpack
 URL: 
 https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
  line 143 in __call__
   app_iter = self.application(environ, start_response)
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
  line 80 in __call__
   return self.application(environ, start_response)
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
  line 91 in __call__
   return self.app( environ, start_response )
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
  line 632 in __call__
   return self.application(environ, start_response)
 File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', 
 line 160 in __call__
   body = method( trans, **kwargs )
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
 line 206 in decorator
   return func( self, trans, *args, **kwargs )
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
  line 1201 in prepare_for_install
   description, repository_clone_url, changeset_revision, ctx_rev, 
 repository_owner, tool_dependencies = repo_info_tuple
 ValueError: too many values to unpack
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 ___
 Please keep all replies on the list by using reply all
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Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

Here is the output from hg heads.

[galaxy@galaxy galaxy-dist]$ hg heads
changeset:   8677:22788c1262a2
tag: tip
user:jeremy goecks jeremy.goe...@emory.edu
date:Mon Jan 28 16:36:02 2013 -0500
summary: Language improvements for tophat wrappers.

changeset:   7987:966a9b393b85
branch:  add_requirement_tags_for_plink
parent:  7472:06b31a61793c
user:Dannon Baker dannonba...@me.com
date:Mon Aug 13 13:23:54 2012 -0400
summary: Branch close

changeset:   7152:ffc20445b35e
branch:  split_blast2
parent:  7058:22f545c0d412
user:Dannon Baker dannonba...@me.com
date:Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.

changeset:   7151:c94957ac5454
branch:  workflow_import_menu_api
parent:  6834:1a3d01b09f7a
user:Dannon Baker dannonba...@me.com
date:Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.

changeset:   7150:314a10ae112d
branch:  split_blast
parent:  6757:ebf65c0b1e26
user:Dannon Baker dannonba...@me.com
date:Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch

changeset:   7149:1327f2219423
branch:  meme_requirement_on_fimo
parent:  6662:8ba74c17e809
user:Daniel Blankenberg d...@bx.psu.edu
date:Fri Feb 03 11:15:29 2012 -0500
summary: close branch


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:00 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

The previous post you mention is outdated.  The main Galaxy tool shed from 
which you are pulling has been tracking Galaxy dist for some time now, so you 
should only have to update to that.

However, the communication layer between Galaxy and the tool shed is backward 
compatible to the December 20, 2012 Galaxy release, so whether you have updated 
from Galaxy central or Galaxy dist, you should not be seeing the behavior you 
describe.

If you do, in fact, track Galaxy central though, and use the main Galaxy tool 
shed, you may experience some strange behavior because the the development code 
may include new features that are not available on the main tool shed since it 
tracks Galaxy dist.

What is the result of typing the following in your Galaxy installation 
directory?

hg heads

Thanks,

Greg Von Kuster


On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote:

Users are getting the following error when trying to add a tool from the tool 
shed repository on our local galaxy instance.

An error occurred. See the error logs for more information. (Turn debug on to 
display exception reports here)

The galaxy server log shows the message included below. The main error is 
ValueError: too many values to unpack . From a similar previous post, the 
resolution was to use the latest code from Galaxy central. I just ran an hg 
pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but 
we still get the same error.

Any ideas?

(server log)
[29/Jan/2013:08:19:05 -0400] GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
 HTTP/1.1 500 - 
http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919;
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, 
like Gecko) Version/5.1.7 Safari/534.57.2
Error - type 'exceptions.ValueError': too many values to unpack
URL: 
https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
File 
'/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
 line 143 in __call__
  app_iter = self.application(environ, start_response)
File 
'/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
 line 80 in __call__
  return self.application(environ, start_response)
File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
 line 91 in __call__
  return self.app( environ, start_response )
File 
'/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
 line 632 in __call__
  return self.application(environ, start_response)
File '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/base.py', 
line 160 in __call__
  body = method( trans, **kwargs )
File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
line 206 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install
  

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Greg Von Kuster]

Hi Michael,

Did you restart your Galaxy server after updating from Galaxy central?  Your 
paster log shows the following:

 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
  line 1201 in prepare_for_install
  description, repository_clone_url, changeset_revision, ctx_rev, 
repository_owner, tool_dependencies = repo_info_tuple

However, that line no longer exists in the revision to which you've updated, 
and line 1201 of the admin_toolshed.py file is now:

status = kwd.get( 'status', 'done' )

Greg Von Kuster


On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

 Here is the output from hg heads.
 
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close
 
 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.
 
 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.
 
 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch
 
 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:00 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 Hi Michael,
 
 The previous post you mention is outdated.  The main Galaxy tool shed from 
 which you are pulling has been tracking Galaxy dist for some time now, so you 
 should only have to update to that.  
 
 However, the communication layer between Galaxy and the tool shed is backward 
 compatible to the December 20, 2012 Galaxy release, so whether you have 
 updated from Galaxy central or Galaxy dist, you should not be seeing the 
 behavior you describe.  
 
 If you do, in fact, track Galaxy central though, and use the main Galaxy tool 
 shed, you may experience some strange behavior because the the development 
 code may include new features that are not available on the main tool shed 
 since it tracks Galaxy dist.
 
 What is the result of typing the following in your Galaxy installation 
 directory?
 
 hg heads
 
 Thanks,
 
 Greg Von Kuster
 
 
 On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote:
 
 Users are getting the following error when trying to add a tool from the 
 tool shed repository on our local galaxy instance.
 
 An error occurred. See the error logs for more information. (Turn debug on 
 to display exception reports here)
 
 The galaxy server log shows the message included below. The main error is 
 ValueError: too many values to unpack . From a similar previous post, the 
 resolution was to use the latest code from Galaxy central. I just ran an hg 
 pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), 
 but we still get the same error.
 
 Any ideas?
 
 (server log)
 [29/Jan/2013:08:19:05 -0400] GET 
 /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
  HTTP/1.1 500 - 
 http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919;
  Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 
 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2
 Error - type 'exceptions.ValueError': too many values to unpack
 URL: 
 https://galaxy.its.unc.edu/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
  line 143 in __call__
   app_iter = self.application(environ, start_response)
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
  line 80 in __call__
   return self.application(environ, start_response)
 File 
 

Re: [galaxy-dev] History not updating automatically

[Sajoscha Sauer]

Hi Nate, 

We have an extra proxy entry for the path galaxy/api, where we also require 
ldap authentication. When I now remove this, the problem with the javascript 
popup is solved and the web is working perfectly fine. 
But now my API is not secured anymore, and this is clearly not what we want. Is 
there a way around that? Or do I just don't get the point? 

My proxy config is: 

RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/g/funcgen/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/(.*) /g/funcgen/galaxy/static/$1 [L]
RewriteRule ^/galaxy/images/(.*) /g/funcgen/galaxy/static/images/$1 [L]
RewriteRule ^/galaxy/upload/(.*) /g/funcgen/galaxy/static/automated_upload/$1 
[L]
RewriteRule ^/galaxy/favicon.ico /g/funcgen/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /g/funcgen/galaxy/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

Location /galaxy
AuthName Galaxy
AuthType Basic
AuthBasicProvider ldap
AuthLDAPURL ldap:/ldap
AuthzLDAPAuthoritative off
Require valid-user
/Location

Location /galaxy/api
AuthName Galaxy (API)
AuthType Basic
AuthBasicProvider ldap
AuthLDAPURL ldap://ldap
AuthzLDAPAuthoritative off
Satisfy any
Allow from all
/Location

Directory /g/funcgen/galaxy/static/automated_upload
AllowOverride Options FileInfo
/Directory

RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e


THanks a lot for your help! 

Cheers, 

Sajoscha


On Jan 28, 2013, at 8:35 PM, Nate Coraor wrote:

 Hi Brad and Sajoscha,
 
 Is there any chance that your proxy configurations are not passing the 
 username in the REMOTE_USER header when the request is to an /api path?  
 Could you provide the relevant portions of your proxy server configs?
 
 Thanks,
 --nate
 
 On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:
 
 Hi Sajoscha:
 
 I have exactly the same problem… it started about a month ago.
 
 Also with external ldap auth.
 
 I have not yet investigated in detail, since it's not crippling - just 
 annoying.
 
 Brad
 
 
 On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
 wrote:
 
 Hi list, 
 
 I have a weird problem after updating to the latest version. 
 
 After doing the update as usual, the history panel is not updating 
 automatically anymore. And when I press refresh, I get an javascript popup 
 saying: 
 
 Error getting history updates from the server.
 Forbidden
 
 
 Also, in the log I see the following: 
 
 galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as 
 '(null)' externally, but has a cookie as 'sa...@embl.de' invalidating 
 session
 
 
 We are using LDAP to connect to Galaxy, but I don't know if this has 
 something to do with the problem. As I said, it was working perfectly fine 
 before the update. 
 
 Does someone know the problem or has any ideas? 
 
 Thanks for your help, 
 
 Sajoscha
 
 
 
 ___
 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/
 
 --
 Brad Langhorst
 langho...@neb.com
 
 
 
 
 
 
 ___
 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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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/

Re: [galaxy-dev] workflow Editor

[sshashi]

Hi  James,
if i want to create  editor only and tools are not required  , can i get
some documents related with galaxy editor . you can send me module name
in galaxy . i can  go through for creating editor .
Regards
shashi

On Mon, 2013-01-28 at 10:55 -0500, James Taylor wrote:
 The client side of the workflow editor is in javascript, using a mix
 of HTML5 Canvas and DOM elements. It communicates with the server
 using JSON. The server side is written in Python. The editor could be
 decoupled and reused, however there are some details that are fairly
 Galaxy specific right now (particularly how tool states -- the values
 of the various input parameters -- are encoded).
 
 --
 James Taylor, Assistant Professor, Biology/CS, Emory University
 
 
 On Mon, Jan 28, 2013 at 5:17 AM,  ssha...@cdac.in wrote:
  Hi,
 
  I want to know about workflow editor and how it works  internally?   what
  type of canvas editor are you using ? doest it support only python
  environment ?
  if  you have any documents related with ,can i get it .
 
  Regards
  shashi
 
  ---
 
  This e-mail is for the sole use of the intended recipient(s) and may
  contain confidential and privileged information. If you are not the
  intended recipient, please contact the sender by reply e-mail and destroy
  all copies and the original message. Any unauthorized review, use,
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  is strictly prohibited and appropriate legal action will be taken.
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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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 Email secured by Check Point
 



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This e-mail is for the sole use of the intended recipient(s) and may
contain confidential and privileged information. If you are not the
intended recipient, please contact the sender by reply e-mail and destroy
all copies and the original message. Any unauthorized review, use,
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Please keep all replies on the list by using reply all
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Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

I had stopped the Galaxy server before running the update, then started it 
afterward.


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:12 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

Did you restart your Galaxy server after updating from Galaxy central?  Your 
paster log shows the following:

File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install
  description, repository_clone_url, changeset_revision, ctx_rev, 
repository_owner, tool_dependencies = repo_info_tuple

However, that line no longer exists in the revision to which you've updated, 
and line 1201 of the admin_toolshed.py file is now:

status = kwd.get( 'status', 'done' )

Greg Von Kuster


On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

Here is the output from hg heads.

[galaxy@galaxy galaxy-dist]$ hg heads
changeset:   8677:22788c1262a2
tag: tip
user:jeremy goecks 
jeremy.goe...@emory.edumailto:jeremy.goe...@emory.edu
date:Mon Jan 28 16:36:02 2013 -0500
summary: Language improvements for tophat wrappers.

changeset:   7987:966a9b393b85
branch:  add_requirement_tags_for_plink
parent:  7472:06b31a61793c
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Mon Aug 13 13:23:54 2012 -0400
summary: Branch close

changeset:   7152:ffc20445b35e
branch:  split_blast2
parent:  7058:22f545c0d412
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.

changeset:   7151:c94957ac5454
branch:  workflow_import_menu_api
parent:  6834:1a3d01b09f7a
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.

changeset:   7150:314a10ae112d
branch:  split_blast
parent:  6757:ebf65c0b1e26
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch

changeset:   7149:1327f2219423
branch:  meme_requirement_on_fimo
parent:  6662:8ba74c17e809
user:Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu
date:Fri Feb 03 11:15:29 2012 -0500
summary: close branch


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:00 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

The previous post you mention is outdated.  The main Galaxy tool shed from 
which you are pulling has been tracking Galaxy dist for some time now, so you 
should only have to update to that.

However, the communication layer between Galaxy and the tool shed is backward 
compatible to the December 20, 2012 Galaxy release, so whether you have updated 
from Galaxy central or Galaxy dist, you should not be seeing the behavior you 
describe.

If you do, in fact, track Galaxy central though, and use the main Galaxy tool 
shed, you may experience some strange behavior because the the development code 
may include new features that are not available on the main tool shed since it 
tracks Galaxy dist.

What is the result of typing the following in your Galaxy installation 
directory?

hg heads

Thanks,

Greg Von Kuster


On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote:

Users are getting the following error when trying to add a tool from the tool 
shed repository on our local galaxy instance.

An error occurred. See the error logs for more information. (Turn debug on to 
display exception reports here)

The galaxy server log shows the message included below. The main error is 
ValueError: too many values to unpack . From a similar previous post, the 
resolution was to use the latest code from Galaxy central. I just ran an hg 
pull -u pointing to galaxy-central (we had been pointing to galaxy-dist), but 
we still get the same error.

Any ideas?

(server log)
[29/Jan/2013:08:19:05 -0400] GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=f19bc86bac946438changeset_revisions=2d6671b10919
 HTTP/1.1 500 - 
http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=f19bc86bac946438changeset_revision=2d6671b10919;
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, 
like Gecko) Version/5.1.7 Safari/534.57.2
Error - type 'exceptions.ValueError': too many values to unpack
URL: 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

To be honest, I barely understand this enough to just follow the wiki 
instructions. When it doesn't work as expected, I'm lost.

I did go back to the output from when I ran the update, and just noticed 
something about not updating because of new heads. What does this mean?

[galaxy@galaxy galaxy-dist]$ hg pull -u
pulling from https://bitbucket.org/galaxy/galaxy-central
searching for changes
adding changesets
adding manifests
adding file changes
added 691 changesets with 2002 changes to 603 files (+1 heads)
not updating, since new heads added
(run 'hg heads' to see heads, 'hg merge' to merge)


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:52 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

Your paster log still is showing the older code.  Any idea how this happens in 
your environment?

On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


I had stopped the Galaxy server before running the update, then started it 
afterward.


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:12 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

Did you restart your Galaxy server after updating from Galaxy central?  Your 
paster log shows the following:

File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install
  description, repository_clone_url, changeset_revision, ctx_rev, 
repository_owner, tool_dependencies = repo_info_tuple

However, that line no longer exists in the revision to which you've updated, 
and line 1201 of the admin_toolshed.py file is now:

status = kwd.get( 'status', 'done' )

Greg Von Kuster


On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

Here is the output from hg heads.

[galaxy@galaxy galaxy-dist]$ hg heads
changeset:   8677:22788c1262a2
tag: tip
user:jeremy goecks 
jeremy.goe...@emory.edumailto:jeremy.goe...@emory.edu
date:Mon Jan 28 16:36:02 2013 -0500
summary: Language improvements for tophat wrappers.

changeset:   7987:966a9b393b85
branch:  add_requirement_tags_for_plink
parent:  7472:06b31a61793c
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Mon Aug 13 13:23:54 2012 -0400
summary: Branch close

changeset:   7152:ffc20445b35e
branch:  split_blast2
parent:  7058:22f545c0d412
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.

changeset:   7151:c94957ac5454
branch:  workflow_import_menu_api
parent:  6834:1a3d01b09f7a
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.

changeset:   7150:314a10ae112d
branch:  split_blast
parent:  6757:ebf65c0b1e26
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch

changeset:   7149:1327f2219423
branch:  meme_requirement_on_fimo
parent:  6662:8ba74c17e809
user:Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu
date:Fri Feb 03 11:15:29 2012 -0500
summary: close branch


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:00 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

The previous post you mention is outdated.  The main Galaxy tool shed from 
which you are pulling has been tracking Galaxy dist for some time now, so you 
should only have to update to that.

However, the communication layer between Galaxy and the tool shed is backward 
compatible to the December 20, 2012 Galaxy release, so whether you have updated 
from Galaxy central or Galaxy dist, you should not be seeing the behavior you 
describe.

If you do, in fact, track Galaxy central though, and use the main Galaxy tool 
shed, you may experience some strange behavior because the the development code 
may include new features that are not available on the main tool shed since it 
tracks Galaxy dist.

What is the result of typing the following in your Galaxy installation 
directory?

hg heads

Thanks,

Greg Von Kuster


On Jan 29, 2013, at 8:38 AM, Waldron, Michael 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Greg Von Kuster]

Have you made some changes to your local Galaxy code base that require merging?

On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote:

 To be honest, I barely understand this enough to just follow the wiki 
 instructions. When it doesn't work as expected, I'm lost.
 
 I did go back to the output from when I ran the update, and just noticed 
 something about not updating because of new heads. What does this mean?
 
 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 Hi Michael,
 
 Your paster log still is showing the older code.  Any idea how this happens 
 in your environment?
 
 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:
 
 
 I had stopped the Galaxy server before running the update, then started it 
 afterward.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 Hi Michael,
 
 Did you restart your Galaxy server after updating from Galaxy central?  Your 
 paster log shows the following:
 
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
  line 1201 in prepare_for_install
   description, repository_clone_url, changeset_revision, ctx_rev, 
 repository_owner, tool_dependencies = repo_info_tuple
 
 However, that line no longer exists in the revision to which you've updated, 
 and line 1201 of the admin_toolshed.py file is now:
 
 status = kwd.get( 'status', 'done' )
 
 Greg Von Kuster
 
 
 On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:
 
 Here is the output from hg heads.
 
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close
 
 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.
 
 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.
 
 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch
 
 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:00 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 Hi Michael,
 
 The previous post you mention is outdated.  The main Galaxy tool shed from 
 which you are pulling has been tracking Galaxy dist for some time now, so 
 you should only have to update to that.  
 
 However, the communication layer between Galaxy and the tool shed is 
 backward compatible to the December 20, 2012 Galaxy release, so whether you 
 have updated from Galaxy central or Galaxy dist, you should not be seeing 
 the behavior you describe.  
 
 If you do, in fact, track Galaxy central though, and use the main Galaxy 
 tool shed, you may experience some strange behavior because the the 
 development code may include new features that are not available on the 
 main tool shed since it tracks Galaxy dist.
 
 What is the result of typing the following in your Galaxy installation 
 directory?
 
 hg heads
 
 Thanks,
 
 Greg Von Kuster
 
 
 On Jan 29, 2013, at 8:38 AM, Waldron, Michael H 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

Not that I know of. We have only edited configuration files and .loc files for 
various tools.

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 10:07 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Have you made some changes to your local Galaxy code base that require merging?

On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote:

To be honest, I barely understand this enough to just follow the wiki 
instructions. When it doesn't work as expected, I'm lost.

I did go back to the output from when I ran the update, and just noticed 
something about not updating because of new heads. What does this mean?

[galaxy@galaxy galaxy-dist]$ hg pull -u
pulling from https://bitbucket.org/galaxy/galaxy-central
searching for changes
adding changesets
adding manifests
adding file changes
added 691 changesets with 2002 changes to 603 files (+1 heads)
not updating, since new heads added
(run 'hg heads' to see heads, 'hg merge' to merge)


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:52 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

Your paster log still is showing the older code.  Any idea how this happens in 
your environment?

On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


I had stopped the Galaxy server before running the update, then started it 
afterward.


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:12 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

Did you restart your Galaxy server after updating from Galaxy central?  Your 
paster log shows the following:

File 
'/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install
  description, repository_clone_url, changeset_revision, ctx_rev, 
repository_owner, tool_dependencies = repo_info_tuple

However, that line no longer exists in the revision to which you've updated, 
and line 1201 of the admin_toolshed.py file is now:

status = kwd.get( 'status', 'done' )

Greg Von Kuster


On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

Here is the output from hg heads.

[galaxy@galaxy galaxy-dist]$ hg heads
changeset:   8677:22788c1262a2
tag: tip
user:jeremy goecks 
jeremy.goe...@emory.edumailto:jeremy.goe...@emory.edu
date:Mon Jan 28 16:36:02 2013 -0500
summary: Language improvements for tophat wrappers.

changeset:   7987:966a9b393b85
branch:  add_requirement_tags_for_plink
parent:  7472:06b31a61793c
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Mon Aug 13 13:23:54 2012 -0400
summary: Branch close

changeset:   7152:ffc20445b35e
branch:  split_blast2
parent:  7058:22f545c0d412
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Wed Apr 18 07:59:38 2012 -0400
summary: Branch close.

changeset:   7151:c94957ac5454
branch:  workflow_import_menu_api
parent:  6834:1a3d01b09f7a
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Wed Mar 21 09:50:44 2012 -0400
summary: Branch close for pull request.

changeset:   7150:314a10ae112d
branch:  split_blast
parent:  6757:ebf65c0b1e26
user:Dannon Baker dannonba...@me.commailto:dannonba...@me.com
date:Tue Feb 28 12:32:54 2012 -0500
summary: Close split_blast branch

changeset:   7149:1327f2219423
branch:  meme_requirement_on_fimo
parent:  6662:8ba74c17e809
user:Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu
date:Fri Feb 03 11:15:29 2012 -0500
summary: close branch


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill


From: Greg Von Kuster [g...@bx.psu.edu]
Sent: Tuesday, January 29, 2013 9:00 AM
To: Waldron, Michael H
Cc: galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Hi Michael,

The previous post you mention is outdated.  The main Galaxy tool shed from 
which you are pulling has been tracking Galaxy dist for some time now, so you 
should only have to update to that.

However, the communication layer between Galaxy and the tool 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Greg Von Kuster]

Perhaps these are the files that have conflicts.  You'll have to get someone 
local that can determine the problems with your environment that are not 
allowing you to get clean updates to your Galaxy code.

On Jan 29, 2013, at 10:11 AM, Waldron, Michael H wrote:

 Not that I know of. We have only edited configuration files and .loc files 
 for various tools.
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 10:07 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 Have you made some changes to your local Galaxy code base that require 
 merging?
 
 On Jan 29, 2013, at 9:57 AM, Waldron, Michael H wrote:
 
 To be honest, I barely understand this enough to just follow the wiki 
 instructions. When it doesn't work as expected, I'm lost.
 
 I did go back to the output from when I ran the update, and just noticed 
 something about not updating because of new heads. What does this mean?
 
 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 Hi Michael,
 
 Your paster log still is showing the older code.  Any idea how this happens 
 in your environment?
 
 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:
 
 
 I had stopped the Galaxy server before running the update, then started it 
 afterward.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 Hi Michael,
 
 Did you restart your Galaxy server after updating from Galaxy central?  
 Your paster log shows the following:
 
 File 
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
  line 1201 in prepare_for_install
   description, repository_clone_url, changeset_revision, ctx_rev, 
 repository_owner, tool_dependencies = repo_info_tuple
 
 However, that line no longer exists in the revision to which you've 
 updated, and line 1201 of the admin_toolshed.py file is now:
 
 status = kwd.get( 'status', 'done' )
 
 Greg Von Kuster
 
 
 On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:
 
 Here is the output from hg heads.
 
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close
 
 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.
 
 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.
 
 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch
 
 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:00 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 Hi Michael,
 
 The previous post you mention is outdated.  The main Galaxy tool shed from 
 which you are pulling has been tracking Galaxy dist for some time now, so 
 you should only have to update to that.  
 
 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[James Taylor]

Can you send the output of hg heads after having run the pull -u ?

Thanks!

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.

 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?

 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)



 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM

 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?

 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


 I had stopped the Galaxy server before running the update, then started it
 afterward.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Did you restart your Galaxy server after updating from Galaxy central?  Your
 paster log shows the following:

 File
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install

   description, repository_clone_url, changeset_revision, ctx_rev,
 repository_owner, tool_dependencies = repo_info_tuple

 However, that line no longer exists in the revision to which you've updated,
 and line 1201 of the admin_toolshed.py file is now:

 status = kwd.get( 'status', 'done' )

 Greg Von Kuster


 On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

 Here is the output from hg heads.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close

 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.

 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.

 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch

 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:00 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 The previous post you mention is outdated.  The main Galaxy tool shed from
 which you are pulling has been tracking Galaxy dist for some time now, so
 you should only have to update to that.

 However, the communication layer between Galaxy and the tool shed is
 backward compatible to the December 20, 2012 Galaxy release, so whether you
 have updated from Galaxy central or Galaxy dist, you should not be seeing
 the behavior you describe.

 If you do, in fact, track Galaxy central though, and use the main Galaxy
 tool shed, you may experience some strange behavior because the the
 development code may include new features that are not available on the main
 tool shed since it tracks Galaxy dist.

 What is the result of typing the following in 

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

[Peter Cock]

On Mon, Jan 28, 2013 at 7:56 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 I've opened a Trello card, but it's in the Galaxy development project, so not 
 sure if you can see it or not.  Here's the link to the card just in case...

 https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/506338ce32ae458f6d15e4b3/182


I can't see that :(

I was wondering about taking a look at this to see how hard it would
be - but my first query is where is the ToolShed source code?

My plan is/was to use this pattern:

http://toolshed.g2.bx.psu.edu/repository/username/
-- All tools by that username

http://toolshed.g2.bx.psu.edu/repository/username/toolname
-- The given tool from that author

This would match the pattern for the the underlying hg repository,
http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler

That would become this for the ToolShed entry:
http://toolshed.g2.bx.psu.edu/repository/peterjc/mira_assembler

Thanks,

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:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

Already in the email thread.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close

 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.

 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.

 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch

 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
[ja...@jamestaylor.org]
Sent: Tuesday, January 29, 2013 11:04 AM
To: Waldron, Michael H
Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Can you send the output of hg heads after having run the pull -u ?

Thanks!

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.

 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?

 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)



 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM

 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?

 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


 I had stopped the Galaxy server before running the update, then started it
 afterward.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Did you restart your Galaxy server after updating from Galaxy central?  Your
 paster log shows the following:

 File
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install

   description, repository_clone_url, changeset_revision, ctx_rev,
 repository_owner, tool_dependencies = repo_info_tuple

 However, that line no longer exists in the revision to which you've updated,
 and line 1201 of the admin_toolshed.py file is now:

 status = kwd.get( 'status', 'done' )

 Greg Von Kuster


 On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

 Here is the output from hg heads.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close

 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

[Peter Cock]

On Tue, Jan 29, 2013 at 4:04 PM, Peter Cock p.j.a.c...@googlemail.com wrote:

 I was wondering about taking a look at this to see how hard it would
 be - but my first query is where is the ToolShed source code?


I think I've found it, in the main repository under the slightly misleading
name of community: lib/galaxy/webapps/community

https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/community

Browsing the files it isn't immediately clear to me how to start... but
I'll spend a bit more time on this today.

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:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Dannon Baker]

You might try an 'hg merge --preview' to see what it actually wants to merge.  
One thing to note is that most of those heads displaying have been pruned and 
newer versions of mercurial will correctly no longer show them.

-Dannon


On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 Already in the email thread.
 
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close
 
 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.
 
 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.
 
 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch
 
 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
 [ja...@jamestaylor.org]
 Sent: Tuesday, January 29, 2013 11:04 AM
 To: Waldron, Michael H
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 Can you send the output of hg heads after having run the pull -u ?
 
 Thanks!
 
 --
 James Taylor, Assistant Professor, Biology/CS, Emory University
 
 
 On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
 mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.
 
 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?
 
 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)
 
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM
 
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository
 
 Hi Michael,
 
 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?
 
 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:
 
 
 I had stopped the Galaxy server before running the update, then started it
 afterward.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository
 
 Hi Michael,
 
 Did you restart your Galaxy server after updating from Galaxy central?  Your
 paster log shows the following:
 
 File
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install
 
  description, repository_clone_url, changeset_revision, ctx_rev,
 repository_owner, tool_dependencies = repo_info_tuple
 
 However, that line no longer exists in the revision to which you've updated,
 and line 1201 of the admin_toolshed.py file is now:
 
 status = kwd.get( 'status', 'done' )
 
 Greg Von Kuster
 
 
 On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:
 
 Here is the output from hg heads.
 
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 changeset:   7987:966a9b393b85
 branch: 

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

[Greg Von Kuster]

Hi Peter,

The tool shed source is mostly in the following places.

~/lib/galaxy/webapps/community/
/lib/galaxy/tool_shed/
/lib/galaxy/util/shed_util_common.py
/lib/galaxy/util/shed_util.py
/template/webapps/community/

I'll get to this as soon as I can, but glad you're willing to take a look.

Greg Von Kuster

On Jan 29, 2013, at 11:04 AM, Peter Cock wrote:

 On Mon, Jan 28, 2013 at 7:56 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 I've opened a Trello card, but it's in the Galaxy development project, so 
 not sure if you can see it or not.  Here's the link to the card just in 
 case...
 
 https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/506338ce32ae458f6d15e4b3/182
 
 
 I can't see that :(
 
 I was wondering about taking a look at this to see how hard it would
 be - but my first query is where is the ToolShed source code?
 
 My plan is/was to use this pattern:
 
 http://toolshed.g2.bx.psu.edu/repository/username/
 -- All tools by that username
 
 http://toolshed.g2.bx.psu.edu/repository/username/toolname
 -- The given tool from that author
 
 This would match the pattern for the the underlying hg repository,
 http://toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler
 
 That would become this for the ToolShed entry:
 http://toolshed.g2.bx.psu.edu/repository/peterjc/mira_assembler
 
 Thanks,
 
 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:
 
  http://lists.bx.psu.edu/


___
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/

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

[Greg Von Kuster]

Yes, the tool shed used to be named the Galaxy Community Space.  

On Jan 29, 2013, at 11:14 AM, Peter Cock wrote:

 On Tue, Jan 29, 2013 at 4:04 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
 
 I was wondering about taking a look at this to see how hard it would
 be - but my first query is where is the ToolShed source code?
 
 
 I think I've found it, in the main repository under the slightly misleading
 name of community: lib/galaxy/webapps/community
 
 https://bitbucket.org/galaxy/galaxy-central/src/default/lib/galaxy/webapps/community
 
 Browsing the files it isn't immediately clear to me how to start... but
 I'll spend a bit more time on this today.
 
 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:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

It doesn't recognize the --preview option.

$ hg merge --preview
hg merge: option --preview not recognized
hg merge [-f] [[-r] REV]


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, January 29, 2013 11:15 AM
To: Waldron, Michael H
Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

You might try an 'hg merge --preview' to see what it actually wants to merge.  
One thing to note is that most of those heads displaying have been pruned and 
newer versions of mercurial will correctly no longer show them.

-Dannon


On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 Already in the email thread.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close

 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.

 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.

 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch

 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
 [ja...@jamestaylor.org]
 Sent: Tuesday, January 29, 2013 11:04 AM
 To: Waldron, Michael H
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

 Can you send the output of hg heads after having run the pull -u ?

 Thanks!

 --
 James Taylor, Assistant Professor, Biology/CS, Emory University


 On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
 mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.

 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?

 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)



 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM

 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?

 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


 I had stopped the Galaxy server before running the update, then started it
 afterward.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Did you restart your Galaxy server after updating from Galaxy central?  Your
 paster log shows the following:

 File
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install

  description, repository_clone_url, changeset_revision, ctx_rev,
 repository_owner, tool_dependencies = repo_info_tuple

 However, that line no longer exists in the revision to which you've updated,
 and line 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Dannon Baker]

Oh fun.  Would it be possible for you to update mercurial?  It might be easier 
to get a handle on what's going on.

Barring that, does 'hg out' show any committed changes that need to go out?

-Dannon


On Jan 29, 2013, at 11:24 AM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 It doesn't recognize the --preview option.
 
 $ hg merge --preview
 hg merge: option --preview not recognized
 hg merge [-f] [[-r] REV]
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 11:15 AM
 To: Waldron, Michael H
 Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 You might try an 'hg merge --preview' to see what it actually wants to merge. 
  One thing to note is that most of those heads displaying have been pruned 
 and newer versions of mercurial will correctly no longer show them.
 
 -Dannon
 
 
 On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:
 
 Already in the email thread.
 
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close
 
 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.
 
 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.
 
 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch
 
 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
 [ja...@jamestaylor.org]
 Sent: Tuesday, January 29, 2013 11:04 AM
 To: Waldron, Michael H
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 Can you send the output of hg heads after having run the pull -u ?
 
 Thanks!
 
 --
 James Taylor, Assistant Professor, Biology/CS, Emory University
 
 
 On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
 mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.
 
 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?
 
 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)
 
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM
 
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository
 
 Hi Michael,
 
 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?
 
 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:
 
 
 I had stopped the Galaxy server before running the update, then started it
 afterward.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository
 
 Hi Michael,
 
 Did you restart your Galaxy server after updating from Galaxy central?  Your
 paster log shows the 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

I'll have to look into updating mercurial. The hg out doesn't show anything to 
be done.

$ hg out
comparing with https://bitbucket.org/galaxy/galaxy-central
searching for changes
no changes found


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, January 29, 2013 11:27 AM
To: Waldron, Michael H
Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Oh fun.  Would it be possible for you to update mercurial?  It might be easier 
to get a handle on what's going on.

Barring that, does 'hg out' show any committed changes that need to go out?

-Dannon


On Jan 29, 2013, at 11:24 AM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 It doesn't recognize the --preview option.

 $ hg merge --preview
 hg merge: option --preview not recognized
 hg merge [-f] [[-r] REV]


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 11:15 AM
 To: Waldron, Michael H
 Cc: James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

 You might try an 'hg merge --preview' to see what it actually wants to merge. 
  One thing to note is that most of those heads displaying have been pruned 
 and newer versions of mercurial will correctly no longer show them.

 -Dannon


 On Jan 29, 2013, at 11:10 AM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:

 Already in the email thread.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close

 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.

 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.

 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch

 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
 [ja...@jamestaylor.org]
 Sent: Tuesday, January 29, 2013 11:04 AM
 To: Waldron, Michael H
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository

 Can you send the output of hg heads after having run the pull -u ?

 Thanks!

 --
 James Taylor, Assistant Professor, Biology/CS, Emory University


 On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
 mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.

 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?

 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)



 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM

 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?

 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


 I had stopped the 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[James Taylor]

Wasn't sure of the order, those are definitely after running the
update. Dannon's advice makes a good point, upgrading to the latest
mercurial should help.

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jan 29, 2013 at 11:10 AM, Waldron, Michael H
mwald...@email.unc.edu wrote:
 Already in the email thread.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  7472:06b31a61793c
 user:Dannon Baker dannonba...@me.com
 date:Mon Aug 13 13:23:54 2012 -0400
 summary: Branch close

 changeset:   7152:ffc20445b35e
 branch:  split_blast2
 parent:  7058:22f545c0d412
 user:Dannon Baker dannonba...@me.com
 date:Wed Apr 18 07:59:38 2012 -0400
 summary: Branch close.

 changeset:   7151:c94957ac5454
 branch:  workflow_import_menu_api
 parent:  6834:1a3d01b09f7a
 user:Dannon Baker dannonba...@me.com
 date:Wed Mar 21 09:50:44 2012 -0400
 summary: Branch close for pull request.

 changeset:   7150:314a10ae112d
 branch:  split_blast
 parent:  6757:ebf65c0b1e26
 user:Dannon Baker dannonba...@me.com
 date:Tue Feb 28 12:32:54 2012 -0500
 summary: Close split_blast branch

 changeset:   7149:1327f2219423
 branch:  meme_requirement_on_fimo
 parent:  6662:8ba74c17e809
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Fri Feb 03 11:15:29 2012 -0500
 summary: close branch


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
 [ja...@jamestaylor.org]
 Sent: Tuesday, January 29, 2013 11:04 AM
 To: Waldron, Michael H
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

 Can you send the output of hg heads after having run the pull -u ?

 Thanks!

 --
 James Taylor, Assistant Professor, Biology/CS, Emory University


 On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
 mwald...@email.unc.edu wrote:
 To be honest, I barely understand this enough to just follow the wiki
 instructions. When it doesn't work as expected, I'm lost.

 I did go back to the output from when I ran the update, and just noticed
 something about not updating because of new heads. What does this mean?

 [galaxy@galaxy galaxy-dist]$ hg pull -u
 pulling from https://bitbucket.org/galaxy/galaxy-central
 searching for changes
 adding changesets
 adding manifests
 adding file changes
 added 691 changesets with 2002 changes to 603 files (+1 heads)
 not updating, since new heads added
 (run 'hg heads' to see heads, 'hg merge' to merge)



 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:52 AM

 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Your paster log still is showing the older code.  Any idea how this happens
 in your environment?

 On Jan 29, 2013, at 9:46 AM, Waldron, Michael H wrote:


 I had stopped the Galaxy server before running the update, then started it
 afterward.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill

 
 From: Greg Von Kuster [g...@bx.psu.edu]
 Sent: Tuesday, January 29, 2013 9:12 AM
 To: Waldron, Michael H
 Cc: galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed
 respository

 Hi Michael,

 Did you restart your Galaxy server after updating from Galaxy central?  Your
 paster log shows the following:

 File
 '/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1201 in prepare_for_install

   description, repository_clone_url, changeset_revision, ctx_rev,
 repository_owner, tool_dependencies = repo_info_tuple

 However, that line no longer exists in the revision to which you've updated,
 and line 1201 of the admin_toolshed.py file is now:

 status = kwd.get( 'status', 'done' )

 Greg Von Kuster


 On Jan 29, 2013, at 9:03 AM, Waldron, Michael H wrote:

 Here is the output from hg heads.

 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 changeset:   7987:966a9b393b85
 branch:  add_requirement_tags_for_plink
 parent:  

[galaxy-dev] Best way to work with one directory and many files as 1 input

[Pierre Pericard]

Hi all,

We've just added some new tools based on R scripts to our local Galaxy 
instance.


Most of these tools need to work at the root of the directory containing 
the input files (up to hundreds of XML files) spread among two or more 
sub-directories. The directory structure need to be kept since the R 
tools recursively search for files and use the subdirectories names as 
classes.


To solve this problem we added a dummy datatype to our instance so we 
can upload the input directory as a zip file without Galaxy 
decompressing it.


datatype extension=dummy_zip type=galaxy.datatypes.data:Data 
mimetype=application/zip display_in_upload=true subclass=true /


However, since our tools can be runned as a workflow and that most of 
them need this input directory we need to unzip it with R in the job 
working directory for each tool (about 5 times for the entire workflow).


Furthermore, this solution doesn't seem very clean if we want to share 
our tools via the ToolShed.


Is there a smart way to handle this kind of input directory that can be 
achieved with Galaxy default datatypes and/or that doesn't require to 
unzip a file each time we use a tool ?


Any update on a behavior change about zip files 
(http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005631.html) ?


Thanks in advance for any input,

Pierre

--
Pierre Pericard
IE CDD - Projet Peptisan

Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
http://abims.sb-roscoff.fr/

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and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

[Peter Cock]

On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 Hi Peter,

 The tool shed source is mostly in the following places.

 ~/lib/galaxy/webapps/community/
 /lib/galaxy/tool_shed/
 /lib/galaxy/util/shed_util_common.py
 /lib/galaxy/util/shed_util.py
 /template/webapps/community/

 I'll get to this as soon as I can, but glad you're willing to take a look.


And according to http://wiki.galaxyproject.org/HostingALocalToolShed
it gets launched via run_community.sh and is configured via
community_wsgi.ini - that makes sense.

This is looking to be a bigger job than I had hoped (given the
learning curve to first understand the way the ToolShed webapp
works).

On Tue, Jan 29, 2013 at 4:18 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 Yes, the tool shed used to be named the Galaxy Community Space.


Presumably at this point changing the name in the code would
break too many things?

Thanks,

Peter
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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:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Best way to work with one directory and many files as 1 input

[Peter Cock]

On Tue, Jan 29, 2013 at 4:41 PM, Pierre Pericard
pierre.peric...@sb-roscoff.fr wrote:
 Hi all,

 We've just added some new tools based on R scripts to our local Galaxy
 instance.

 Most of these tools need to work at the root of the directory containing the
 input files (up to hundreds of XML files) spread among two or more
 sub-directories. The directory structure need to be kept since the R tools
 recursively search for files and use the subdirectories names as classes.

 To solve this problem we added a dummy datatype to our instance so we can
 upload the input directory as a zip file without Galaxy decompressing it.

Have you looked at a composite datatype instead, where the files are
stored on disk decompressed?

http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes

Peter
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Best way to work with one directory and many files as 1 input

[Pierre Pericard]

If I'm not mistaking, Composite Datatypes allow for only one directory, 
whereas we need to keep a constant directory structure with 2 or more 
sub-directories containing our input files.


We have no way to change these tools behavior (obviously not 
Galaxy-friendly ;-) ) and therefore need to maintain this structure in 
the job working directory.


Pierre.


Pierre Pericard
IE CDD - Projet Peptisan

Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
http://abims.sb-roscoff.fr/

Le 29/01/2013 17:47, Peter Cock a écrit :

On Tue, Jan 29, 2013 at 4:41 PM, Pierre Pericard
pierre.peric...@sb-roscoff.fr wrote:

Hi all,

We've just added some new tools based on R scripts to our local Galaxy
instance.

Most of these tools need to work at the root of the directory containing the
input files (up to hundreds of XML files) spread among two or more
sub-directories. The directory structure need to be kept since the R tools
recursively search for files and use the subdirectories names as classes.

To solve this problem we added a dummy datatype to our instance so we can
upload the input directory as a zip file without Galaxy decompressing it.

Have you looked at a composite datatype instead, where the files are
stored on disk decompressed?

http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes

Peter


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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:

 http://lists.bx.psu.edu/

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Paul Boddie]

On 29/01/13 17:33, James Taylor wrote:

Wasn't sure of the order, those are definitely after running the
update. Dannon's advice makes a good point, upgrading to the latest
mercurial should help.


If upgrading Mercurial will involve introducing another detour, you 
could potentially check which version of the Galaxy code you're using 
now as defined by the parent revisions:


hg parents

This (or these in certain cases) might not be a repository head and 
thus won't appear in hg heads. If you have the graphlog extension 
enabled, running the following might be informative as it should show 
you where you are (with a @ symbol) in the code history:


hg glog | more

If you don't want to risk your working directory, you could first clone 
it to make something that you can then experiment with:


hg clone . ../galaxy-dist-test

Then, you'd move into this clone:

cd ../galaxy-dist-test

You might need to update to the version previously printed by hg 
parents above:


hg update revision

One might then assume that any desirable update would involve getting to 
the tip, and so you could try a merge with that:


hg merge tip

If all of this works reasonably, you should be able to do the same merge 
on your real working directory (and can thus delete the test directory). 
The result of any merge will need to be committed:


hg commit

Anyway, these are just some thoughts. The crucial point is that you can 
clone the repository and then work with the clone, discarding it if your 
experiments go wrong. Doing this might be quicker than having to get a 
more recent Mercurial version installed.


Paul
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Re: [galaxy-dev] Best way to work with one directory and many files as 1 input

[Peter Cock]

On Tue, Jan 29, 2013 at 4:58 PM, Pierre Pericard
pierre.peric...@sb-roscoff.fr wrote:
 If I'm not mistaking, Composite Datatypes allow for only one directory,
 whereas we need to keep a constant directory structure with 2 or more
 sub-directories containing our input files.

I'm not sure if that is true - the example of HTML output with images
comes to mind as a common use-case where subfolder(s) would be
expected. I've only had limited first hand experience with Galaxy's
composite datatypes myself though.

 We have no way to change these tools behavior (obviously not Galaxy-friendly
 ;-) ) and therefore need to maintain this structure in the job working
 directory.

Perhaps a tool wrapper could create a dummy folder using symlinks
(faster and less wasted disk than copying files), but that isn't ideal.

Peter
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Re: [galaxy-dev] Can't browse big library anymore (web and API)

[Sajoscha Sauer]

Hi again, 

So, we just found out that one of our automatically launched scripts had a bug 
and was creating library datasets over and over again. Ending up in 16000+ 
entries of the same library dataset before it started to fail. 
That's not at all a solution to the problem but brings me to another question 
:) 

Because we cannot use the web interface anymore to delete them, is there a way 
to remove all these library datasets from the database? 
Would it work to flag them deleted and use the purge scripts to locate and 
remove the associated files? And after that, which database tables do we have 
to clean in order to remove the library datasets completely from the database? 


Thanks a lot, 

Sajoscha

On Jan 29, 2013, at 3:47 PM, Sajoscha Sauer wrote:

 Dear all, 
 
 We have a really annoying problem with one of our Libraries: we can't access 
 it anymore. We think the problem might be that the library contains too many 
 folders/files (the error message is pasted at the end of the mail). 
 
 Is there any limit for library content ? Note that we can still browse 
 smaller libraries, so I though that we should simply split the library into 
 smaller ones but since we can t even browse it...Any suggestions how to 
 approach this problem?
 
 We are running a galaxy instance used by different research groups and our 
 current setup is the following: 
 - we have one Library per research group
 - we create a folder per project, under the relevant library, and add all 
 files in these folders. Note that we add symbolic links to the real file 
 locations (this way the large fastq files remain on owners file servers)
 - the files are transferred automatically to Galaxy using custom code that 
 makes use of the galaxy API. 
 
 And of course, this automated transfer now crashes as our custom code tries 
 to read library content thru API call (to ask the user in which folder the 
 new files should be added)
 
 PS: browsing libraries in general is really slow and gives users a bad 'user 
 experience' (not mentioning all the extra clicks they issue because they 
 think Galaxy did not get the request...), I am not sure why this action is 
 that slow ( browsing small size library is also slow). I think I saw emails 
 about this issue but I am not sure what the status is?  Is there anything we 
 could do in the code to speed this up? I am not sure this problem is related 
 to the current post , so sorry for mixing things up.
 
 Thanks for your help!
 
 Cheers
 
 Sajoscha
 
 
 
 === error on galaxy page (nothing in the galaxy log file)
 
 error.tiff
 
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Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

Forgot to also include the hg parents output.

$ hg parents
changeset:   7986:12fcd068b12e
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job action.


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Waldron, Michael H
Sent: Tuesday, January 29, 2013 1:28 PM
To: Paul Boddie; James Taylor
Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository

As it turns out, it was fairly simple to install a newer hg version (2.4.2).

So now running hg merger --preview and hg heads returns:

$ hg merge --preview
abort: branch 'default' has one head - please merge with an explicit rev
(run 'hg heads' to see all heads)
[galaxy@galaxy galaxy-dist]$ hg heads
changeset:   8677:22788c1262a2
tag: tip
user:jeremy goecks jeremy.goe...@emory.edu
date:Mon Jan 28 16:36:02 2013 -0500
summary: Language improvements for tophat wrappers.

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Paul Boddie [paul.bod...@biotek.uio.no]
Sent: Tuesday, January 29, 2013 12:01 PM
To: James Taylor
Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

On 29/01/13 17:33, James Taylor wrote:
 Wasn't sure of the order, those are definitely after running the
 update. Dannon's advice makes a good point, upgrading to the latest
 mercurial should help.

If upgrading Mercurial will involve introducing another detour, you
could potentially check which version of the Galaxy code you're using
now as defined by the parent revisions:

hg parents

This (or these in certain cases) might not be a repository head and
thus won't appear in hg heads. If you have the graphlog extension
enabled, running the following might be informative as it should show
you where you are (with a @ symbol) in the code history:

hg glog | more

If you don't want to risk your working directory, you could first clone
it to make something that you can then experiment with:

hg clone . ../galaxy-dist-test

Then, you'd move into this clone:

cd ../galaxy-dist-test

You might need to update to the version previously printed by hg
parents above:

hg update revision

One might then assume that any desirable update would involve getting to
the tip, and so you could try a merge with that:

hg merge tip

If all of this works reasonably, you should be able to do the same merge
on your real working directory (and can thus delete the test directory).
The result of any merge will need to be committed:

hg commit

Anyway, these are just some thoughts. The crucial point is that you can
clone the repository and then work with the clone, discarding it if your
experiments go wrong. Doing this might be quicker than having to get a
more recent Mercurial version installed.

Paul

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Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Dannon Baker]

So that's interesting.  My best guess was that this was caused by swapping from 
galaxy-dist to galaxy-central in the situation where galaxy-dist has had 
changesets applied directly and then ported to galaxy-central out of order, 
combined with your oder version of mercurial.  That parent, however, would have 
been before that happened.

Anyway, at this point, does `hg update --check` actually work?

And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, 
http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be 
faster to iterate through what we need to do to get your repository back in 
shape.


On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 Forgot to also include the hg parents output.
 
 $ hg parents
 changeset:   7986:12fcd068b12e
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Thu Oct 18 11:22:12 2012 -0400
 summary: Do not hide failed datasets with HideDatasetAction post job 
 action.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Waldron, Michael H
 Sent: Tuesday, January 29, 2013 1:28 PM
 To: Paul Boddie; James Taylor
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository
 
 As it turns out, it was fairly simple to install a newer hg version (2.4.2).
 
 So now running hg merger --preview and hg heads returns:
 
 $ hg merge --preview
 abort: branch 'default' has one head - please merge with an explicit rev
 (run 'hg heads' to see all heads)
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Paul Boddie [paul.bod...@biotek.uio.no]
 Sent: Tuesday, January 29, 2013 12:01 PM
 To: James Taylor
 Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 On 29/01/13 17:33, James Taylor wrote:
 Wasn't sure of the order, those are definitely after running the
 update. Dannon's advice makes a good point, upgrading to the latest
 mercurial should help.
 
 If upgrading Mercurial will involve introducing another detour, you
 could potentially check which version of the Galaxy code you're using
 now as defined by the parent revisions:
 
 hg parents
 
 This (or these in certain cases) might not be a repository head and
 thus won't appear in hg heads. If you have the graphlog extension
 enabled, running the following might be informative as it should show
 you where you are (with a @ symbol) in the code history:
 
 hg glog | more
 
 If you don't want to risk your working directory, you could first clone
 it to make something that you can then experiment with:
 
 hg clone . ../galaxy-dist-test
 
 Then, you'd move into this clone:
 
 cd ../galaxy-dist-test
 
 You might need to update to the version previously printed by hg
 parents above:
 
 hg update revision
 
 One might then assume that any desirable update would involve getting to
 the tip, and so you could try a merge with that:
 
 hg merge tip
 
 If all of this works reasonably, you should be able to do the same merge
 on your real working directory (and can thus delete the test directory).
 The result of any merge will need to be committed:
 
 hg commit
 
 Anyway, these are just some thoughts. The crucial point is that you can
 clone the repository and then work with the clone, discarding it if your
 experiments go wrong. Doing this might be quicker than having to get a
 more recent Mercurial version installed.
 
 Paul
 
 ___
 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 subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

The hg update --check command reports the following:

$ hg update --check
abort: uncommitted local changes

I just connected to the #galaxyproject IRC channel.


Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, January 29, 2013 1:37 PM
To: Waldron, Michael H
Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

So that's interesting.  My best guess was that this was caused by swapping from 
galaxy-dist to galaxy-central in the situation where galaxy-dist has had 
changesets applied directly and then ported to galaxy-central out of order, 
combined with your oder version of mercurial.  That parent, however, would have 
been before that happened.

Anyway, at this point, does `hg update --check` actually work?

And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, 
http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be 
faster to iterate through what we need to do to get your repository back in 
shape.


On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 Forgot to also include the hg parents output.

 $ hg parents
 changeset:   7986:12fcd068b12e
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Thu Oct 18 11:22:12 2012 -0400
 summary: Do not hide failed datasets with HideDatasetAction post job 
 action.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: Waldron, Michael H
 Sent: Tuesday, January 29, 2013 1:28 PM
 To: Paul Boddie; James Taylor
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: RE: [galaxy-dev] Error trying to add tools from tool shed respository

 As it turns out, it was fairly simple to install a newer hg version (2.4.2).

 So now running hg merger --preview and hg heads returns:

 $ hg merge --preview
 abort: branch 'default' has one head - please merge with an explicit rev
 (run 'hg heads' to see all heads)
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.

 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: Paul Boddie [paul.bod...@biotek.uio.no]
 Sent: Tuesday, January 29, 2013 12:01 PM
 To: James Taylor
 Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

 On 29/01/13 17:33, James Taylor wrote:
 Wasn't sure of the order, those are definitely after running the
 update. Dannon's advice makes a good point, upgrading to the latest
 mercurial should help.

 If upgrading Mercurial will involve introducing another detour, you
 could potentially check which version of the Galaxy code you're using
 now as defined by the parent revisions:

 hg parents

 This (or these in certain cases) might not be a repository head and
 thus won't appear in hg heads. If you have the graphlog extension
 enabled, running the following might be informative as it should show
 you where you are (with a @ symbol) in the code history:

 hg glog | more

 If you don't want to risk your working directory, you could first clone
 it to make something that you can then experiment with:

 hg clone . ../galaxy-dist-test

 Then, you'd move into this clone:

 cd ../galaxy-dist-test

 You might need to update to the version previously printed by hg
 parents above:

 hg update revision

 One might then assume that any desirable update would involve getting to
 the tip, and so you could try a merge with that:

 hg merge tip

 If all of this works reasonably, you should be able to do the same merge
 on your real working directory (and can thus delete the test directory).
 The result of any merge will need to be committed:

 hg commit

 Anyway, these are just some thoughts. The crucial point is that you can
 clone the repository and then work with the clone, discarding it if your
 experiments go wrong. Doing this might be quicker than having to get a
 more recent Mercurial version installed.

 Paul

 ___
 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 subscriptions to this
and other Galaxy lists, please use the interface at:

  

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Dannon Baker]

I don't know why I thought we'd already checked this, but --

'hg st' will tell you which files have been modified in your local repository, 
and
'hg diff' will tell you exactly what changes have taken place

I'm not sure of the exact state of your repository at the moment, so this 
*might* display all changes from the pull as well, which wouldn't be 
particularly useful.  Worth trying, though.

Don't see you in #galaxyproject yet, sure it's working?


On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 The hg update --check command reports the following:
 
 $ hg update --check
 abort: uncommitted local changes
 
 I just connected to the #galaxyproject IRC channel.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 1:37 PM
 To: Waldron, Michael H
 Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 So that's interesting.  My best guess was that this was caused by swapping 
 from galaxy-dist to galaxy-central in the situation where galaxy-dist has had 
 changesets applied directly and then ported to galaxy-central out of order, 
 combined with your oder version of mercurial.  That parent, however, would 
 have been before that happened.
 
 Anyway, at this point, does `hg update --check` actually work?
 
 And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, 
 http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be 
 faster to iterate through what we need to do to get your repository back in 
 shape.
 
 
 On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:
 
 Forgot to also include the hg parents output.
 
 $ hg parents
 changeset:   7986:12fcd068b12e
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Thu Oct 18 11:22:12 2012 -0400
 summary: Do not hide failed datasets with HideDatasetAction post job 
 action.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Waldron, Michael H
 Sent: Tuesday, January 29, 2013 1:28 PM
 To: Paul Boddie; James Taylor
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: RE: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 As it turns out, it was fairly simple to install a newer hg version (2.4.2).
 
 So now running hg merger --preview and hg heads returns:
 
 $ hg merge --preview
 abort: branch 'default' has one head - please merge with an explicit rev
 (run 'hg heads' to see all heads)
 [galaxy@galaxy galaxy-dist]$ hg heads
 changeset:   8677:22788c1262a2
 tag: tip
 user:jeremy goecks jeremy.goe...@emory.edu
 date:Mon Jan 28 16:36:02 2013 -0500
 summary: Language improvements for tophat wrappers.
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Paul Boddie [paul.bod...@biotek.uio.no]
 Sent: Tuesday, January 29, 2013 12:01 PM
 To: James Taylor
 Cc: Waldron, Michael H; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 On 29/01/13 17:33, James Taylor wrote:
 Wasn't sure of the order, those are definitely after running the
 update. Dannon's advice makes a good point, upgrading to the latest
 mercurial should help.
 
 If upgrading Mercurial will involve introducing another detour, you
 could potentially check which version of the Galaxy code you're using
 now as defined by the parent revisions:
 
 hg parents
 
 This (or these in certain cases) might not be a repository head and
 thus won't appear in hg heads. If you have the graphlog extension
 enabled, running the following might be informative as it should show
 you where you are (with a @ symbol) in the code history:
 
 hg glog | more
 
 If you don't want to risk your working directory, you could first clone
 it to make something that you can then experiment with:
 
 hg clone . ../galaxy-dist-test
 
 Then, you'd move into this clone:
 
 cd ../galaxy-dist-test
 
 You might need to update to the version previously printed by hg
 parents above:
 
 hg update revision
 
 One might then assume that any desirable update would involve getting to
 the tip, and so you could try a merge with that:
 
 hg merge tip
 
 If all of this works reasonably, you should be able to do the same merge
 on your real working directory (and can thus delete the test directory).
 The result of any merge will need to be committed:
 
 hg commit
 
 Anyway, these are just some thoughts. The crucial point is that you can
 clone the repository and then work with the clone, discarding it if your
 experiments go wrong. 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

Here is hg st output:

$ hg st
M scripts/cleanup_datasets/delete_datasets.sh
M scripts/cleanup_datasets/delete_datasets_main.sh
M scripts/cleanup_datasets/delete_userless_histories.sh
M scripts/cleanup_datasets/delete_userless_histories_main.sh
M scripts/cleanup_datasets/purge_datasets.sh
M scripts/cleanup_datasets/purge_datasets_main.sh
M scripts/cleanup_datasets/purge_folders.sh
M scripts/cleanup_datasets/purge_folders_main.sh
M scripts/cleanup_datasets/purge_histories.sh
M scripts/cleanup_datasets/purge_histories_main.sh
M scripts/cleanup_datasets/purge_libraries.sh
M scripts/cleanup_datasets/purge_libraries_main.sh
M scripts/cleanup_datasets/update_metadata.sh
M tools/peak_calling/macs_wrapper.xml
M tools/plotting/boxplot.xml
M tools/sr_mapping/bfast_wrapper.xml
M tools/sr_mapping/bowtie2_wrapper.xml
M tools/sr_mapping/bowtie_color_wrapper.xml
M tools/sr_mapping/bowtie_wrapper.xml
M tools/sr_mapping/bwa_color_wrapper.xml
M tools/sr_mapping/bwa_wrapper.xml
? contrib/galaxy-init
? galaxy_cleanup.log
? galaxy_cleanup.sh
? migrated_tools_conf.xml.110712
? paster.pid
? scripts/cleanup_datasets/delete_userless_histories.log
? scripts/cleanup_datasets/purge_datasets.log
? scripts/cleanup_datasets/purge_folders.log
? scripts/cleanup_datasets/purge_histories.log
? scripts/cleanup_datasets/purge_libraries.log
? static/UNC_galaxy_mirror_housekeeping_notes.pdf
? tool-data/bwa_index.loc.sample
? tool-data/bwa_index_color.loc.sample
? tool-data/tool_data_table_conf.xml.sample
? tool_conf.xml.110212
? tool_conf.xml.new
? tool_data_table_conf.xml.030112
? tools/plotting/boxplot.xml.012512
? typescript

The hg diff output is quite long.

It turns out I didn't connect to the IRC channel. I have XChat IRC client, but 
not familiar with using it. How to I connect to the irc.freenode.net server to 
access the #galaxyproject channel?

Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, January 29, 2013 1:48 PM
To: Waldron, Michael H
Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

I don't know why I thought we'd already checked this, but --

'hg st' will tell you which files have been modified in your local repository, 
and
'hg diff' will tell you exactly what changes have taken place

I'm not sure of the exact state of your repository at the moment, so this 
*might* display all changes from the pull as well, which wouldn't be 
particularly useful.  Worth trying, though.

Don't see you in #galaxyproject yet, sure it's working?


On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 The hg update --check command reports the following:

 $ hg update --check
 abort: uncommitted local changes

 I just connected to the #galaxyproject IRC channel.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 1:37 PM
 To: Waldron, Michael H
 Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

 So that's interesting.  My best guess was that this was caused by swapping 
 from galaxy-dist to galaxy-central in the situation where galaxy-dist has had 
 changesets applied directly and then ported to galaxy-central out of order, 
 combined with your oder version of mercurial.  That parent, however, would 
 have been before that happened.

 Anyway, at this point, does `hg update --check` actually work?

 And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, 
 http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be 
 faster to iterate through what we need to do to get your repository back in 
 shape.


 On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:

 Forgot to also include the hg parents output.

 $ hg parents
 changeset:   7986:12fcd068b12e
 user:Daniel Blankenberg d...@bx.psu.edu
 date:Thu Oct 18 11:22:12 2012 -0400
 summary: Do not hide failed datasets with HideDatasetAction post job 
 action.


 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: Waldron, Michael H
 Sent: Tuesday, January 29, 2013 1:28 PM
 To: Paul Boddie; James Taylor
 Cc: Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: RE: [galaxy-dev] Error trying to add tools from tool shed 
 respository

 As it turns out, it was fairly simple to install a newer hg version (2.4.2).

 So now running hg merger --preview and hg heads returns:

 $ hg merge --preview
 abort: branch 'default' has one head - please merge with an explicit rev
 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Dannon Baker]

Ok, so that confirms that you definitely have local customizations we'll want 
to make sure to keep.  What I'd do before we go any further is this:

`hg diff -p  local_changes.patch`

This will save all of your current changes to a patch, should we have to 
recreate them (though I don't expect this).

`hg ci -m Local changes to cleanup_datasets and various tools`

Which will commit your local changes to your local repository.  At this point, 
hopefully, you can just 'hg update', possibly needing to merge as well.

For IRC:  Just join the Freenode network shown in XChat, and then Join 
Channel should pop up a box you can put #galaxyproject in



On Jan 29, 2013, at 1:52 PM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 Here is hg st output:
 
 $ hg st
 M scripts/cleanup_datasets/delete_datasets.sh
 M scripts/cleanup_datasets/delete_datasets_main.sh
 M scripts/cleanup_datasets/delete_userless_histories.sh
 M scripts/cleanup_datasets/delete_userless_histories_main.sh
 M scripts/cleanup_datasets/purge_datasets.sh
 M scripts/cleanup_datasets/purge_datasets_main.sh
 M scripts/cleanup_datasets/purge_folders.sh
 M scripts/cleanup_datasets/purge_folders_main.sh
 M scripts/cleanup_datasets/purge_histories.sh
 M scripts/cleanup_datasets/purge_histories_main.sh
 M scripts/cleanup_datasets/purge_libraries.sh
 M scripts/cleanup_datasets/purge_libraries_main.sh
 M scripts/cleanup_datasets/update_metadata.sh
 M tools/peak_calling/macs_wrapper.xml
 M tools/plotting/boxplot.xml
 M tools/sr_mapping/bfast_wrapper.xml
 M tools/sr_mapping/bowtie2_wrapper.xml
 M tools/sr_mapping/bowtie_color_wrapper.xml
 M tools/sr_mapping/bowtie_wrapper.xml
 M tools/sr_mapping/bwa_color_wrapper.xml
 M tools/sr_mapping/bwa_wrapper.xml
 ? contrib/galaxy-init
 ? galaxy_cleanup.log
 ? galaxy_cleanup.sh
 ? migrated_tools_conf.xml.110712
 ? paster.pid
 ? scripts/cleanup_datasets/delete_userless_histories.log
 ? scripts/cleanup_datasets/purge_datasets.log
 ? scripts/cleanup_datasets/purge_folders.log
 ? scripts/cleanup_datasets/purge_histories.log
 ? scripts/cleanup_datasets/purge_libraries.log
 ? static/UNC_galaxy_mirror_housekeeping_notes.pdf
 ? tool-data/bwa_index.loc.sample
 ? tool-data/bwa_index_color.loc.sample
 ? tool-data/tool_data_table_conf.xml.sample
 ? tool_conf.xml.110212
 ? tool_conf.xml.new
 ? tool_data_table_conf.xml.030112
 ? tools/plotting/boxplot.xml.012512
 ? typescript
 
 The hg diff output is quite long.
 
 It turns out I didn't connect to the IRC channel. I have XChat IRC client, 
 but not familiar with using it. How to I connect to the irc.freenode.net 
 server to access the #galaxyproject channel?
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 1:48 PM
 To: Waldron, Michael H
 Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository
 
 I don't know why I thought we'd already checked this, but --
 
 'hg st' will tell you which files have been modified in your local 
 repository, and
 'hg diff' will tell you exactly what changes have taken place
 
 I'm not sure of the exact state of your repository at the moment, so this 
 *might* display all changes from the pull as well, which wouldn't be 
 particularly useful.  Worth trying, though.
 
 Don't see you in #galaxyproject yet, sure it's working?
 
 
 On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:
 
 The hg update --check command reports the following:
 
 $ hg update --check
 abort: uncommitted local changes
 
 I just connected to the #galaxyproject IRC channel.
 
 
 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill
 
 
 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 1:37 PM
 To: Waldron, Michael H
 Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed 
 respository
 
 So that's interesting.  My best guess was that this was caused by swapping 
 from galaxy-dist to galaxy-central in the situation where galaxy-dist has 
 had changesets applied directly and then ported to galaxy-central out of 
 order, combined with your oder version of mercurial.  That parent, however, 
 would have been before that happened.
 
 Anyway, at this point, does `hg update --check` actually work?
 
 And, lastly, If you want -- hop on IRC (irc.freenode.net #galaxyproject, 
 http://wiki.galaxyproject.org/Get%20Involved#IRC_Channel) and it might be 
 faster to iterate through what we need to do to get your repository back in 
 shape.
 
 
 On Jan 29, 2013, at 1:32 PM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:
 
 Forgot to also include the hg parents output.
 
 $ hg parents
 

Re: [galaxy-dev] Error trying to add tools from tool shed respository

[Waldron, Michael H]

With Dannon's help, I was able to straighten out our local installation by 
doing the following:

Update mercurial to new version (2.4.2) for hg to work as expected.

Commit local changes:
  hg diff -p  local_changes.patch  (save local changes as a patch, in case 
needed)
  hg ci -m Local changes to cleanup_datasets and various tools  (commit 
changes)

hg update   (no files unresolved)

hg tip  (shows latest update)

hg heads  (shows 2 heads so need to merge)

hg merge

hg ci -m Merged changes  (commit merged changes)

hg head  (only 1 head now)

Restarted server, ran the needed database migration script and option tool 
migration script.

The instance is now successfully updated, and this fixed the original problem 
of not being able to install a tool from the tool shed.



Mike Waldron
Systems Specialist
ITS - Research Computing Center
University of North Carolina at Chapel Hill



From: Dannon Baker [dannonba...@me.com]
Sent: Tuesday, January 29, 2013 2:04 PM
To: Waldron, Michael H
Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev
Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

Ok, so that confirms that you definitely have local customizations we'll want 
to make sure to keep.  What I'd do before we go any further is this:

`hg diff -p  local_changes.patch`

This will save all of your current changes to a patch, should we have to 
recreate them (though I don't expect this).

`hg ci -m Local changes to cleanup_datasets and various tools`

Which will commit your local changes to your local repository.  At this point, 
hopefully, you can just 'hg update', possibly needing to merge as well.

For IRC:  Just join the Freenode network shown in XChat, and then Join 
Channel should pop up a box you can put #galaxyproject in



On Jan 29, 2013, at 1:52 PM, Waldron, Michael H mwald...@email.unc.edu 
wrote:

 Here is hg st output:

 $ hg st
 M scripts/cleanup_datasets/delete_datasets.sh
 M scripts/cleanup_datasets/delete_datasets_main.sh
 M scripts/cleanup_datasets/delete_userless_histories.sh
 M scripts/cleanup_datasets/delete_userless_histories_main.sh
 M scripts/cleanup_datasets/purge_datasets.sh
 M scripts/cleanup_datasets/purge_datasets_main.sh
 M scripts/cleanup_datasets/purge_folders.sh
 M scripts/cleanup_datasets/purge_folders_main.sh
 M scripts/cleanup_datasets/purge_histories.sh
 M scripts/cleanup_datasets/purge_histories_main.sh
 M scripts/cleanup_datasets/purge_libraries.sh
 M scripts/cleanup_datasets/purge_libraries_main.sh
 M scripts/cleanup_datasets/update_metadata.sh
 M tools/peak_calling/macs_wrapper.xml
 M tools/plotting/boxplot.xml
 M tools/sr_mapping/bfast_wrapper.xml
 M tools/sr_mapping/bowtie2_wrapper.xml
 M tools/sr_mapping/bowtie_color_wrapper.xml
 M tools/sr_mapping/bowtie_wrapper.xml
 M tools/sr_mapping/bwa_color_wrapper.xml
 M tools/sr_mapping/bwa_wrapper.xml
 ? contrib/galaxy-init
 ? galaxy_cleanup.log
 ? galaxy_cleanup.sh
 ? migrated_tools_conf.xml.110712
 ? paster.pid
 ? scripts/cleanup_datasets/delete_userless_histories.log
 ? scripts/cleanup_datasets/purge_datasets.log
 ? scripts/cleanup_datasets/purge_folders.log
 ? scripts/cleanup_datasets/purge_histories.log
 ? scripts/cleanup_datasets/purge_libraries.log
 ? static/UNC_galaxy_mirror_housekeeping_notes.pdf
 ? tool-data/bwa_index.loc.sample
 ? tool-data/bwa_index_color.loc.sample
 ? tool-data/tool_data_table_conf.xml.sample
 ? tool_conf.xml.110212
 ? tool_conf.xml.new
 ? tool_data_table_conf.xml.030112
 ? tools/plotting/boxplot.xml.012512
 ? typescript

 The hg diff output is quite long.

 It turns out I didn't connect to the IRC channel. I have XChat IRC client, 
 but not familiar with using it. How to I connect to the irc.freenode.net 
 server to access the #galaxyproject channel?

 Mike Waldron
 Systems Specialist
 ITS - Research Computing Center
 University of North Carolina at Chapel Hill


 
 From: Dannon Baker [dannonba...@me.com]
 Sent: Tuesday, January 29, 2013 1:48 PM
 To: Waldron, Michael H
 Cc: Paul Boddie; James Taylor; Greg Von Kuster; galaxy-...@bx.psu.edu Dev
 Subject: Re: [galaxy-dev] Error trying to add tools from tool shed respository

 I don't know why I thought we'd already checked this, but --

 'hg st' will tell you which files have been modified in your local 
 repository, and
 'hg diff' will tell you exactly what changes have taken place

 I'm not sure of the exact state of your repository at the moment, so this 
 *might* display all changes from the pull as well, which wouldn't be 
 particularly useful.  Worth trying, though.

 Don't see you in #galaxyproject yet, sure it's working?


 On Jan 29, 2013, at 1:42 PM, Waldron, Michael H mwald...@email.unc.edu 
 wrote:

 The hg update --check command reports the following:

 $ hg update --check
 abort: uncommitted local changes

 I just connected to the #galaxyproject IRC channel.


 Mike Waldron
 Systems Specialist
 ITS - 

Re: [galaxy-dev] Only custom genomes for uploads in data libraries

[Carlos Borroto]

On Mon, Jan 28, 2013 at 10:40 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
 On Sun, Jan 27, 2013 at 10:04 AM, Jeremy Goecks jeremy.goe...@emory.edu 
 wrote:

 Actually, there an easier way to fix this without patching your Galaxy 
 installation. Builds will show up in the library dbkey box if there's a 
 chromosome length file associated with the build. Chromosome length files 
 are used in some format converters (e.g. wig/bedgraph-to-bigwig) and for 
 visualization.

 You can download len files by doing the following:

 (1) Uncomment/add len_file_path to your universe.wsgi.ini file, e.g.:

 len_file_path = tool-data/shared/ucsc/chrom


 (2) Run these commands from your Galaxy install to download len files from 
 UCSC:

 mkdir ./tool-data/shared/ucsc/chrom/
 python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/

 (3) Restart Galaxy.


 Thanks Jeremy, I will try this and report back.

I can confirm following these steps fix this issue.

Thanks a lot,
Carlos

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[galaxy-dev] Problem referencing EMBOSS tools in universe_wsgi.ini

[Guest, Simon]

We have set up our local Galaxy installation to submit jobs by default through 
HTCondor, using the drmaa tool runner.  We override this on a tool-by-tool 
basis in universe_wsgi.ini, to specify certain tools we always want to run 
locally.

The problem is that EMBOSS tools have a tool id like 'emboss: infoseq46', and 
it's not possible to reference a tool with an id containing a colon in the 
universe_wsgi.ini file (because colon is the character which separates a 
configuration item name from its value).

It seems to me there are two possible solutions:
1. Implement some form of escape character processing in the config file parser 
(on top of Python's ConfigParser) so we can write tool ids in that file like 
'emboss%3a infoseq46'
2. Change all the EMBOSS tools to have ids like 'emboss-infoseq46' rather than 
using a colon and space.

For now, we are modifying our XML files locally (with a script) to do 2.

Are there any comments from Galaxy developers on which of these solutions they 
prefer, or any reason why (2) shouldn't be incorporated in the Galaxy mainline?

cheers,
Simon


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[galaxy-dev] Job handler : crash

[Christophe Caron]

Hello,

We run Galaxy (2013 January version) with load balancing mode (5 x web 
manager, 5 job handler) with Apache/Sun Grid Engine 6.0u4/CentOS 6.3


- Since 2 weeks, some handler job process crash during the Galaxy 
startup with this error message in handlerx.log


.
Starting server in PID 13634.
serving on http://127.0.0.1:8091
galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 Stopping job 22842:
galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 stopping job 22842 in 
drmaa runner



 - The system log files report a segfault with libdrmaa

kernel: python[13977]: segfault at 0 ip 7f2811805dc5 sp 
7f27f4aac0a0 error 4 in libdrmaa.so.1.0[7f28116dd000+185000]




Thanks for your help !

Christophe

--

Christophe Caron

Station Biologique / Service Informatique et Bio-informatique
Place Georges Teissier - CS 90074
29688 Roscoff Cedex

Analysis and Bioinformatics for Marine Science
   http://abims.sb-roscoff.fr/

christophe.ca...@sb-roscoff.fr

tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77






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Re: [galaxy-dev] Job handler : crash

[Derrick Lin]

Hi, I had the similar issue a while ago, and it's fixed in

https://bitbucket.org/galaxy/galaxy-central/commits/c015b82b3944f967e2c859d5552c00e3e38a2da0

Hope this help
D


On Wed, Jan 30, 2013 at 9:39 AM, Christophe Caron 
christophe.ca...@sb-roscoff.fr wrote:

 Hello,

 We run Galaxy (2013 January version) with load balancing mode (5 x web
 manager, 5 job handler) with Apache/Sun Grid Engine 6.0u4/CentOS 6.3

 - Since 2 weeks, some handler job process crash during the Galaxy startup
 with this error message in handlerx.log

 .
 Starting server in PID 13634.
 serving on http://127.0.0.1:8091
 galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 Stopping job 22842:
 galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 stopping job 22842 in
 drmaa runner


  - The system log files report a segfault with libdrmaa

 kernel: python[13977]: segfault at 0 ip 7f2811805dc5 sp
 7f27f4aac0a0 error 4 in libdrmaa.so.1.0[7f28116dd000+**185000]



 Thanks for your help !

 Christophe

 --

 Christophe Caron

 Station Biologique / Service Informatique et Bio-informatique
 Place Georges Teissier - CS 90074
 29688 Roscoff Cedex

 Analysis and Bioinformatics for Marine Science
http://abims.sb-roscoff.fr/

 christophe.ca...@sb-roscoff.fr

 tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77






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[galaxy-dev] sort the list of users while impersonating a user.

[Luobin Yang]

Hi,

The list of users is not sorted when I try to impersonate a user, this is
very inconvenient because of the large number of users in the system, is
there a quick way to have users sorted ?

Thanks,
Luobin
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Re: [galaxy-dev] workflows stop prematurely

[mark.rose]

Ok, I added
track_jobs_in_database = True

to universe_wsgi.ini and now workflows appear to go to completion.

Another problem I was having was that steps in a workflow would stay gray even 
though examination of the log revealed the steps had completed and produced 
correct output (as verified by directly opening the dat files).  This problem 
also seems to have been fixed by the above.

Mark

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of mark.r...@syngenta.com
Sent: Monday, January 28, 2013 1:18 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] workflows stop prematurely

Hi All

On my local install of galaxy I'm having  problems executing workflows.  I will 
upload data into a new history and then select to run a saved workflow.  This 
initiates fine but, after the completion of a variable number of steps, the 
workflow just stops after the successful completion of a step.  No errors 
appear in the web interface and all I can see in the paster.log is something 
like


90 HTTP/1.1 200 - http://127.0.0.1:8081/history; Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0
127.0.0.1 - - [28/Jan/2013:12:29:07 -0400] GET /api/histories/82b264d8c3d11790 
HTTP/1.1 200 - http://127.0.0.1:8081/history; Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0
galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:08,621 execution finished: 
python 
/home/rosema1/Projects/galaxy-dist/tools/fastq/fastq_trimmer_by_quality.py 
'/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_590.dat' 
'/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_592.dat' -f 
'sanger' -s '5'  -t '1' -e '53' -a 'mean' -x '0' -c '=' -q '20.0'
galaxy.jobs DEBUG 2013-01-28 12:29:08,838 Tool did not define exit code or 
stdio handling; checking stderr for success
galaxy.tools DEBUG 2013-01-28 12:29:09,135 Error opening galaxy.json file: 
[Errno 2] No such file or directory: 
'/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/418/galaxy.json'
galaxy.jobs DEBUG 2013-01-28 12:29:09,439 job 418 ended
galaxy.jobs DEBUG 2013-01-28 12:29:10,041 (420) Working directory for job is: 
/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420
galaxy.jobs.handler DEBUG 2013-01-28 12:29:10,042 dispatching job 420 to local 
runner
galaxy.jobs.handler INFO 2013-01-28 12:29:10,200 (420) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:10,385 Local runner: starting 
job 420
galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:10,759 executing: python 
/home/rosema1/Projects/galaxy-dist/tools/fastq/fastq_filter.py 
/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_592.dat 
/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420/tmph0Ll2V
 /home/rosema1/Projects/galaxy-dist/database/files/000/dataset_594.dat 
/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420/dataset_594_files
 'sanger'
127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] GET /api/histories/82b264d8c3d11790 
HTTP/1.1 200 - http://127.0.0.1:8081/history; Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0
127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] GET /api/users/f2db41e1fa331b3e 
HTTP/1.1 200 - http://127.0.0.1:8081/history; Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0
127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] GET 
/api/histories/82b264d8c3d11790/contents?ids=3da459a26c8f00b4%2C736af8f0a76a2e71
 HTTP/1.1 200 - http://127.0.0.1:8081/history; Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0

127.0.0.1 - - [28/Jan/2013:12:29:16 -0400] GET /api/histories/82b264d8c3d11790 
HTTP/1.1 200 - http://127.0.0.1:8081/history; Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0

Though I seem to see this even when a step completes and the workflow proceeds.

Moreover, if I then begin executing the next steps in the workflow, they work, 
but create new entries in the history.

So, some questions:

Why is this happening and what can I do to get workflows to run to completion?

Also,  is it possible to reinitiate the workflow from the premature stopping 
point without having to launch each step individually and point each at new 
inputs rather than the ones dictated in the workflow?

Thanks

Mark






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[galaxy-dev] Different behavior of select tag in the tool configuration file when the number of options is different.

[Luobin Yang]

Hi,

I have a 'select' tag in a tool's XML file, I would like to have a default
option, which is choosing nothing. So the drop down menu of the web
interface will be empty and when a user clicks the drop down menu, the list
contains an empty entry with other options. So I basically have an option
tag like the following option value=/option together with other
options. This works fine when I have up to 19 options including the default
options. A user can submit the job without selecting any options and the
program will use the default option. However, when the number of options
exceeds 20, then drop down menu of the web interface displays Click to
Select or Search instead of empty. And the user has to select one of the
options in order to submit the job, otherwise, a question mark is displayed
in the drop down menu and then an error message shows up under the drop
down menu with the message An invalid option was selected, please verify.
Why the behavior changed when there are 20 options or more for a drop down
menu?

Thanks,
Luobin
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