[galaxy-dev] Fwd: tophat job will not start

2012-09-10 Thread Yun Li 
Hi --

I have an alignment job submitted to tophat using galaxy and the job
has said that it is waiting to start for the last day. My other jobs
have been running and completed and this has continued to be displayed
as waiting to run. Can you please help explain or address this?

Thank you,

--
Yun Rose Li
MD/PhD Trainee, CD3
Perelman School of Medicine
University of Pennsylvania
Philadelphia, PA 19104


-- 
Yun Rose Li
MD/PhD Trainee, CD3
Perelman School of Medicine
University of Pennsylvania
Philadelphia, PA 19104
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Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-10 Thread Dave Bouvier 

Derrick,

The deferred_job_queue instance in the job manager object is only 
instantiated when the enable_beta_job_managers variable is set to True. 
Is it possible that your previous setting of that variable was somehow 
reverted?


The KeyError error you mentioned in your previous should be fixed in the 
latest -dist and -central revisions.


   --Dave B.

On 9/9/12 21:20:44.000, Derrick Lin wrote:

Hi guys,

I found that the problematic loc files were created by CloudBioLinux and
point to the reference indexes downloaded by CloudBioLinux script. I
suspect that Manage Local Data cannot recognize the file structure
created by CloudBioLinux?

Anyhow, I removed all the loc files from CloudBioLinux, then Manage
Local Data can run now. Soon after I tried to download the bowtie hg18
from ucsc, I was given another error caused by deferred job queue:

URL: http://129.94.136.11:8080/galaxy_dev/data_admin/download_build
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
   app_iter = self.application(environ, detect_start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
   environ, self.app)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
   app_iter = application(environ, replacement_start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
   return self.application(environ, start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
   return self.application(environ, start_response)
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
   body = method( trans, **kwargs )
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py',
line 184 in decorator
   return func( self, trans, *args, **kwargs )
File
'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py',
line 199 in download_build
   jobid =
trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job(
trans, url, dbkey, longname, indexers )
AttributeError: 'JobManager' object has no attribute 'deferred_job_queue'

Anyone can give some hints about what was going on?

Regards,
Derrick

On Fri, Sep 7, 2012 at 4:26 PM, Derrick Lin klin...@gmail.com
mailto:klin...@gmail.com wrote:

Hi guys,

I enabled the tool with enable_beta_job_managers = True, server runs
fine. But after I clicked on Manage local data, it gave the
following error:

URL:
http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data [^
http://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data]
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
   app_iter = self.application(environ, detect_start_response)
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
   environ, self.app)
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
   app_iter = application(environ, replacement_start_response)
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
   return self.application(environ, start_response)
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
   return self.application(environ, start_response)
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
   body = method( trans, **kwargs )
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/framework/__init__.py',
line 184 in decorator
   return func( self, trans, *args, **kwargs )
File

'/misc/PWBCAdminStore/app/galaxy/galaxy_dist/dev/lib/galaxy/web/controllers/data_admin.py',
line 47 in manage_data
   genomes[ dbkey ][ table ] = dict( state='Generated',
style=self.jobstyles[ 'done' ] )
KeyError: 'phix'

I tried to fix it by commenting out all the phix entries in all .loc
files. Then it gave the same error but this time caused by hg18. I
think it must have something to do with builts.txt,
manual_builts.txt and the loc files?

Thanks
Derrick




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Re: [galaxy-dev] cuffdiff output: FPKM value zero

2012-09-10 Thread graham etherington (TSL) 
Hi Suzan,
The problem here is that there's an absence of data for one of the genes
you want to compare, so one can't really assign any significance to that
particular gene or transcript.
This would require inventing a singificance value where if a gene is
highly expressed in one sample, but not measured at all in another, then
that gene should be said to be significantly differentially expressed.
If you are looking for situations like this I see no reason why you can't
create a rule for identifying them and pulling them out of the cuffdiff
results.
Even then, you'll have to make some decision about what FPKM value would
be significantly different from 0 in another.
Hope this helps.
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 07/09/2012 16:16, suzan katie suz.ka...@gmail.com wrote:




Hello everyone,

I am comparing two samples (control and treated) paired end RNA Seq data.
In the cuffdiff output I have noticed that few genes have zero FPKM value
in one sample and other sample has significant FPKM value.

I want to identify uniquely expressed genes identified only in one sample
(either control or treated).


My question: If something is measured with significance in one sample
(high FPKM), but not measured at all in another sample (Zero FPKM),
should I consider that gene as significant?

Can anyone explain this.

Thanks

suz






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Re: [galaxy-dev] purging unused datasets and histories

2012-09-10 Thread graham etherington (TSL) 
Hi Nikhil,
Purging datasets is covered in the Galaxy Wiki.

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%
20Datasets


Basically, there's a bunch of scripts in
{GALAXY_HOME}/scripts/cleanup_datasets/ that require running.

We've created a single .sh file that executes all these scripts which is
then executed itself with a cron job at midnight (and of course can be
executed whenever required).
Cheers,
Graham


Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 09/09/2012 11:29, Nikhil Joshi najo...@ucdavis.edu wrote:

Hi all,

I'm a little confused about all the purging scripts what I want to
do is purge all of the unused datasets and histories and keep the
saved or published datasets, histories and workflows and data
libraries.  Which script do I use to do that?

- Nik.

-- 
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
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[galaxy-dev] problem in Fastq tool

2012-09-10 Thread Felix Homa 
Hello,

 

We noticed a problem with the tool Filter Fastq. It seemed to mishandle the
paired-end checkbox. Here is the XML which seems to not work:

 

  param name=paired_end label=This is paired end data type=boolean
truevalue=paired_end falsevalue=single_end checked=False/

 

Concretely, $paired_end.value return True or False as value and not
paired_end or single_end, so in the python code execution,

 

#if $paired_end.value == 'single_end':

 qual_scores_split = [ qual_scores ]

#else:

 qual_scores_split = [ qual_scores[ 0:int( len( qual_scores ) / 2 ) ],
qual_scores[ int( len( qual_scores ) / 2 ): ]]

 

Always go in the else, always splitting reads even when they are single_end.

 

It induces wrong results in our read filtering.

 

I hope the explanation is clear enough

 

Best regards,

 

Felix

 

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[galaxy-dev] Toolshed is not starting + patch

2012-09-10 Thread Björn Grüning 
Hi,

the toolshed is not starting with the latest galaxy-central version.
Attached is a small patch to solve that problem.

Cheers,
Bjoern

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/
diff -r 9207ba35fa0c templates/webapps/community/base_panels.mako
--- a/templates/webapps/community/base_panels.mako	Sun Sep 09 18:24:51 2012 -0400
+++ b/templates/webapps/community/base_panels.mako	Mon Sep 10 18:18:52 2012 +0200
@@ -72,7 +72,7 @@
 ## Help tab.
 %
 menu_options = [  
-[_('Galaxy QA'), app.config.get( qa_url, http://slyfox.bx.psu.edu:8080/; ), _blank ]
+[_('Galaxy QA'), app.config.get( qa_url, http://slyfox.bx.psu.edu:8080/; ), _blank ],
 [_('Support'), app.config.get( support_url, http://wiki.g2.bx.psu.edu/Support; ), _blank ],
 [_('Tool shed wiki'), app.config.get( wiki_url, http://wiki.g2.bx.psu.edu/Tool%20Shed; ), _blank ],
 [_('Galaxy wiki'), app.config.get( wiki_url, http://wiki.g2.bx.psu.edu/; ), _blank ],
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Re: [galaxy-dev] Toolshed is not starting + patch

2012-09-10 Thread Greg Von Kuster 
Hi Bjorn,

The main Galaxy tool shed is tracking the Galaxy-dist repository.  Per requests 
from the Galaxy community, it no longer tracks Galaxy-central.

Greg Von Kuster

On Sep 10, 2012, at 12:25 PM, Björn Grüning wrote:

 Hi,
 
 the toolshed is not starting with the latest galaxy-central version.
 Attached is a small patch to solve that problem.
 
 Cheers,
 Bjoern
 
 -- 
 Björn Grüning
 Albert-Ludwigs-Universität Freiburg
 Institute of Pharmaceutical Sciences
 Pharmaceutical Bioinformatics
 Hermann-Herder-Strasse 9
 D-79104 Freiburg i. Br.
 
 Tel.:  +49 761 203-4872
 Fax.:  +49 761 203-97769
 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
 Web: http://www.pharmaceutical-bioinformatics.org/
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Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository

2012-09-10 Thread Greg Von Kuster 
Hello Birgit,

It looks like you are attempting to install from the test Galaxy tool shed, 
which tracks fairly closely to the Galaxy central repository on bitbucket.  
What changeset revision of Galaxy are you running?  It will always speed up our 
handling of issues like this if you include this information in your initial 
emails in the future.

The main Galaxy tool shed now track the Galaxy dist repository on bitbucket.

Thanks,

Greg Von Kuster

On Sep 10, 2012, at 3:44 PM, Birgit Crain wrote:

 Hi 
 
 I got a problem with the tool_data_table.xml and tool-data/*.loc files when 
 testing the download of my repository.
 
 My repository contains a *.loc.sample file and a 
 tool_data_table_conf.xml.sample (they were unchanged from my last upload to 
 the repository).
 When installing the repository I get the following messages:
 
 172.22.128.28 - - [10/Sep/2012:11:46:16 -0700] GET 
 /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F
  HTTP/1.1 302 - http://lx-galaxy-1:8080/admin_toolshed/browse_tool_sheds; 
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
 Firefox/15.0.1
 172.22.128.28 - - [10/Sep/2012:11:46:39 -0700] GET 
 /admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=96d1ef4698eaa22dchangeset_revisions=982e19c29ec0
  HTTP/1.1 200 - 
 http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=96d1ef4698eaa22dchangeset_revision=982e19c29ec0webapp=galaxy;
  Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
 Firefox/15.0.1
 Adding new row (or updating an existing row) for repository 
 'testing_cgatools' in the tool_shed_repository table.
 galaxy.web.controllers.admin_toolshed DEBUG 2012-09-10 11:47:27,751 Appending 
 to tool panel section: CG tools
 172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] POST 
 /admin_toolshed/prepare_for_install?encoded_repo_info_dicts=606805d7b3160cf8502df2b105df5510f61a250c%3A7b2274657374696e675f636761746f6f6c73223a205b22746869732069732061207465737420222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f62637261696e2d636f6d706c65746567656e6f6d6963732f74657374696e675f636761746f6f6c73222c2022393832653139633239656330222c20223233222c202262637261696e2d636f6d706c65746567656e6f6d696373222c206e756c6c5d7dincludes_tools=Truetool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2Fincludes_tool_dependencies=False
  HTTP/1.1 302 - 
 http://lx-galaxy-1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=96d1ef4698eaa22dchangeset_revisions=982e19c29ec0;
  Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
 Firefox/15.0.1
 172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] GET 
 /admin_toolshed/initiate_repository_installation?shed_repository_ids=f2db41e1fa331b3ereinstalling=Falseencoded_kwd=80e690a1cf32f1294e27873f210c5344dc427413%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
  HTTP/1.1 200 - 
 http://lx-galaxy-1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=96d1ef4698eaa22dchangeset_revisions=982e19c29ec0;
  Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
 Firefox/15.0.1
 172.22.128.28 - - [10/Sep/2012:11:47:31 -0700] POST 
 /admin_toolshed/repository_installation_status_updates HTTP/1.1 200 -

Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository

2012-09-10 Thread Birgit Crain 
I downloaded the latest galaxy-dist this morning and I used the test toolshed 
to test my repository first before I upload it to the main toolshed.
Thanks

Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, 
Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.commailto:bcr...@completegenomics.com


From: Greg Von Kuster g...@bx.psu.edumailto:g...@bx.psu.edu
Date: Monday, September 10, 2012 1:06 PM
To: Birgit Crain 
bcr...@completegenomics.commailto:bcr...@completegenomics.com
Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with 
repository

Hello Birgit,

It looks like you are attempting to install from the test Galaxy tool shed, 
which tracks fairly closely to the Galaxy central repository on bitbucket.  
What changeset revision of Galaxy are you running?  It will always speed up our 
handling of issues like this if you include this information in your initial 
emails in the future.

The main Galaxy tool shed now track the Galaxy dist repository on bitbucket.

Thanks,

Greg Von Kuster

On Sep 10, 2012, at 3:44 PM, Birgit Crain wrote:

Hi

I got a problem with the tool_data_table.xml and tool-data/*.loc files when 
testing the download of my repository.

My repository contains a *.loc.sample file and a 
tool_data_table_conf.xml.sample (they were unchanged from my last upload to the 
repository).
When installing the repository I get the following messages:

172.22.128.28 - - [10/Sep/2012:11:46:16 -0700] GET 
/admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F
 HTTP/1.1 302 - http://lx-galaxy-1:8080/admin_toolshed/browse_tool_sheds; 
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
Firefox/15.0.1
172.22.128.28 - - [10/Sep/2012:11:46:39 -0700] GET 
/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=96d1ef4698eaa22dchangeset_revisions=982e19c29ec0
 HTTP/1.1 200 - 
http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=96d1ef4698eaa22dchangeset_revision=982e19c29ec0webapp=galaxy;
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
Firefox/15.0.1
Adding new row (or updating an existing row) for repository 'testing_cgatools' 
in the tool_shed_repository table.
galaxy.web.controllers.admin_toolshed DEBUG 2012-09-10 11:47:27,751 Appending 
to tool panel section: CG tools
172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] POST 
/admin_toolshed/prepare_for_install?encoded_repo_info_dicts=606805d7b3160cf8502df2b105df5510f61a250c%3A7b2274657374696e675f636761746f6f6c73223a205b22746869732069732061207465737420222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f62637261696e2d636f6d706c65746567656e6f6d6963732f74657374696e675f636761746f6f6c73222c2022393832653139633239656330222c20223233222c202262637261696e2d636f6d706c65746567656e6f6d696373222c206e756c6c5d7dincludes_tools=Truetool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2Fincludes_tool_dependencies=False
 HTTP/1.1 302 - 
http://lx-galaxy-1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=96d1ef4698eaa22dchangeset_revisions=982e19c29ec0;
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 
Firefox/15.0.1
172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] GET

Re: [galaxy-dev] disk space warning

2012-09-10 Thread Edward Kirton 
i use a cron job to monitor my disks and email me if they approach capacity.
i'm not sure of the benefit of informing your users; better for a sysop to
take care of it before it becomes a problem.
i also use cron jobs to purge older files from the ftp and tmp dirs.


On Thu, Sep 6, 2012 at 6:48 AM, Mutlu Dogruel mutludogr...@gmail.comwrote:

 Hi, is there a way to warn users when the disk becomes full during a
 URL-based file upload (and local file upload)? I had to manually delete the
 temp files created during a large upload that hanged, after which Galaxy
 could not be re-started due to insufficient disk space.

 Thanks.

 --
 Mutlu


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[galaxy-dev] fastQC report bug

2012-09-10 Thread David Hoover 
Hi,

I have a very recent version of Galaxy installed locally, and when I run 
FastQC:Read QC, it creates an HTML file with missing links to the plots and 
images within the HTML.  The HTML source looks identical to the HTML source 
from the main Galaxy server, so there must be something wrong with my local 
install.

Is there some option or modification that I need to enable to allow access to 
the generated HTML/PNG files in the database/files/000/database_###_files 
directory?

David Hoover
Helix Systems Staff
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Re: [galaxy-dev] Manage local data admin tool failed with dbkey KeyError

2012-09-10 Thread Derrick Lin 
Hi Dave,

The  enable_beta_job_managers is set to true in my universe ini file.
Unless it can be override in somewhere else?

My galaxy hasn't been patched to the Sep release, but will give it a try.

I actually also downloaded the complete pre-built indexes from galaxy's
recent released rsync server. I am wondering if the Manage data tool
recognizes those downloaded indexes and avoid downloading again from uscs
server?

Derrick

On Mon, Sep 10, 2012 at 10:59 PM, Dave Bouvier d...@bx.psu.edu wrote:

 Derrick,

 The deferred_job_queue instance in the job manager object is only
 instantiated when the enable_beta_job_managers variable is set to True. Is
 it possible that your previous setting of that variable was somehow
 reverted?

 The KeyError error you mentioned in your previous should be fixed in the
 latest -dist and -central revisions.

--Dave B.


 On 9/9/12 21:20:44.000, Derrick Lin wrote:

 Hi guys,

 I found that the problematic loc files were created by CloudBioLinux and
 point to the reference indexes downloaded by CloudBioLinux script. I
 suspect that Manage Local Data cannot recognize the file structure
 created by CloudBioLinux?

 Anyhow, I removed all the loc files from CloudBioLinux, then Manage
 Local Data can run now. Soon after I tried to download the bowtie hg18
 from ucsc, I was given another error caused by deferred job queue:

 URL: 
 http://129.94.136.11:8080/**galaxy_dev/data_admin/**download_buildhttp://129.94.136.11:8080/galaxy_dev/data_admin/download_build
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 WebError-0.8a-py2.6.egg/**weberror/evalexception/**middleware.py',
 line 364 in respond
app_iter = self.application(environ, detect_start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**debug/prints.py',
 line 98 in __call__
environ, self.app)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**wsgilib.py',
 line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**recursive.py',
 line 80 in __call__
return self.application(environ, start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**httpexceptions.py',
 line 632 in __call__
return self.application(environ, start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/lib/**
 galaxy/web/framework/base.py',
 line 160 in __call__
body = method( trans, **kwargs )
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/lib/**
 galaxy/web/framework/__init__.**py',
 line 184 in decorator
return func( self, trans, *args, **kwargs )
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/lib/**
 galaxy/web/controllers/data_**admin.py',
 line 199 in download_build
jobid =
 trans.app.job_manager.**deferred_job_queue.plugins['**
 GenomeTransferPlugin'].create_**job(
 trans, url, dbkey, longname, indexers )
 AttributeError: 'JobManager' object has no attribute 'deferred_job_queue'

 Anyone can give some hints about what was going on?

 Regards,
 Derrick

 On Fri, Sep 7, 2012 at 4:26 PM, Derrick Lin klin...@gmail.com
 mailto:klin...@gmail.com wrote:

 Hi guys,

 I enabled the tool with enable_beta_job_managers = True, server runs
 fine. But after I clicked on Manage local data, it gave the
 following error:

 URL:
 
 http://pwbc.garvan.unsw.edu.**au/galaxy_dev/data_admin/**manage_datahttp://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data[^
 
 http://pwbc.garvan.unsw.edu.**au/galaxy_dev/data_admin/**manage_datahttp://pwbc.garvan.unsw.edu.au/galaxy_dev/data_admin/manage_data
 ]

 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 WebError-0.8a-py2.6.egg/**weberror/evalexception/**middleware.py',
 line 364 in respond
app_iter = self.application(environ, detect_start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**debug/prints.py',
 line 98 in __call__
environ, self.app)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**wsgilib.py',
 line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**recursive.py',
 line 80 in __call__
return self.application(environ, start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/eggs/**
 Paste-1.6-py2.6.egg/paste/**httpexceptions.py',
 line 632 in __call__
return self.application(environ, start_response)
 File
 '/misc/PWBCAdminStore/app/**galaxy/galaxy_dist/dev/lib/**
 galaxy/web/framework/base.py',
 line 160 in __call__
body = method( trans, **kwargs

[galaxy-dev] HYPHY tools

2012-09-10 Thread Julian Pradinuk 
Hi all,

Could someone please point me to helpful ressources for installing HYPHY in
Galaxy?


   - I've downloaded, compiled and installed HyPhy
   - I've copied the contents of the installation folder to
   .../galaxy-dist/tool-data/HYPHY
   - I've symlinked HYPHYMP in that folder to HYPHY
   - I uncommented the print statement in /usr/local/galaxy/develop/
   galaxy-dist/tools/hyphy/hyphy_nj_tree_wrapper.py and the standard output
   from running in Galaxy now reads:

Single Alignment Analyses
 Error:
 Could not read command file in ExecuteAFile.
 Original path: '/usr/local/galaxy/develop/galaxy-dist/tool-data/HYPHY/
 TemplateBatchFiles/chooseDistanceFormula.def'.
 Expanded path: '/usr/local/galaxy/develop/galaxy-dist/tool-data/HYPHY/
 TemplateBatchFiles/chooseDistanceFormula.def'
 Function call stack
 1 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+
 TemplateBatchFiles+DIRECTORY_SEPARATOR+chooseDistanceFormula.def using
 basepath /tmp/.
 Standard input redirect:
 1 : TN93
 2 : /galaxy_data/develop/files/000/dataset_285.dat
 3 : /tmp/tmpuKVPrQ
 ---
 2 : InferTreeTopology(0)
 Standard input redirect:
 1 : TN93
 2 : /galaxy_data/develop/files/000/dataset_285.dat
 3 : /tmp/tmpuKVPrQ
 ---
 3 : ExecuteAFile from file /tmp/tmpdu4x8_ using basepath /tmp/. reading
 input from _genomeScreenOptions
 {0:/galaxy_data/develop/files/000/dataset_260.dat,
 1:TN93,
 2:/galaxy_data/develop/files/000/dataset_285.dat,
 3:/tmp/tmpuKVPrQ}
 ---


Any help would be greatly appreciated!

Thanks!

Julian
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[galaxy-dev] Doodle Poll for September Galaxy Users Group Meeting

2012-09-10 Thread Ann Black-Ziegelbein 
Hi everyone!

We are targeting a web conference for our second Galaxy Deployers/Operators
group meeting for the last two weeks of September.  The time we set for the
September meeting I would like to use as a template for future meetings.
(EG 3rd Monday at 9 am central time).   Please take a moment to fill out the
doodle poll with all times you would be available to participate in such a
call ­ this will help us choose the best day/time for the majority.

http://doodle.com/wxzxxaqgf942gi43

Once again, this teleconference will be held using Elluminate
Live/Blackboard Collborate web conference - so all data (including voice)
will be over the internet. It seemed to hold up well during our first web
conference and we can record our session and post it for playback off of the
wiki.  We have posted the recording of our last conference on our group wiki
page:

http://wiki.g2.bx.psu.edu/Community/GalaxyCzars


Here is a draft agenda for our September call - comments are welcome :

September Mtg.

* Name change!  GalaxyCzars may not fit us right Š please bring your
suggestions or email them ahead of time.  We will provide a virtual toast to
the winning suggestion!
* Presentation: Alex Moskalenko will present on the University of Florida's
Galaxy and experiences with migrating to the latest Galaxy release.
* Open Mic: Bring your problems, your successes, and questions for
discussion.

Thanks so much! 

Ann

Ann Black-Ziegelbein
Senior Application Developer
University of Iowa 
Center for Bioinformatics and Computational Biology
Iowa Institute for Human Genetics



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