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
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The previous post you mention is outdated.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
, 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
' 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
, 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
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
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
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
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
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
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
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
We get the following error when trying to run MACS in our local installation of
Galaxy:
INFO @ Mon, 30 Apr 2012 09:02:14:
# ARGUMENTS LIST:
# name = MACS_in_Galaxy
# ChIP-seq file = /proj/galaxy/000/dataset_552.dat
# control file = None
# effective genome size = 2.70e+09
# tag size = 36
# band
On our local installation of Galaxy, we get the following error when running
Macs:
Usage: macs -t tfile [-n name] [-g genomesize] [options]
Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks
macs: error: no such option: --lambdaset
What is the latest version of
-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Waldron, Michael H [mwald...@email.unc.edu]
Sent: Thursday, March 01, 2012 8:56 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Error trying to enable samtools_mpileup
I am running a local copy of Galaxy, last
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