Hi Simon!
Hi all,
I've been trying to get my velvet optimiser wrapper to automatically
install the tool and its dependencies to no avail.
Nice!
Here is my problem in detail.
I have what I thought would be a simple wrapper and tool to pack into
the new toolshed.
I have a
Dear Developers,
I am running GATK for first time. In galaxy i use Unified Genotyper. I am
getting error as below mentioned.
# ERROR
--
# ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
Hi Lance,
I can confirm both the regression and the fix. A pull request would be
great I think. I can also do it if you want.
Thanks,
Björn
The recent updates to set_user_disk_usage.py for Postgres users have
an issue with Postgres 8.x. The SQL in the pgcalc method (line 51)
leads to the
Hi Sridhar,
About the error, you need to request a key from GATK
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
See under How to obtain and use a GATK key
Or by pass it by removing the -et NO_ET line from the xml files.
From:
Hi,
I want to select a date from a calender in my tool, but I think that it's not
possible in the xml. I was looking for some examples with xml, javascript and
jquery but I could not do what I wanted. My code is:
tool id=idPlot name=Plot
command interpreter=bashr_wrapper.sh
Thanks for confirmation Björn.
Pull request was submitted:
https://bitbucket.org/galaxy/galaxy-central/pull-request/97/fix-for-postgres-versions-9/diff
Trello card also created: https://trello.com/c/Z0EynAV2
Björn Grüning wrote:
Hi Lance,
I can confirm both the regression and the fix. A
Thanks for the bug fix, (and for the reminder that it was still sitting in
the inbox, sorry about that). I've verified the fix as well and pulled it
into -central.
-Dannon
On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons lpars...@princeton.eduwrote:
Thanks for confirmation Björn.
Pull
Just wanted to mention that the Get the latest copy [..] section at
http://wiki.galaxyproject.org/Admin/Get%20Galaxy should have the user cd into
galaxy-dist before performing hg update stable.
Sincerely,
Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia
Instructor
On Jun 5, 2013, at 10:01 PM, Adam Brenner wrote:
Why not use Allow All / Deny All rules?
Location /
... your Auth Type stuff here ...
Deny from all
Allow from 127.0.0.1 # Assuming API calls are made locally
Satisfy any
/Location
You shouldn't need to restrict to just the
On Jun 6, 2013, at 10:34 AM, Michael E. Cotterell wrote:
Just wanted to mention that the Get the latest copy [..] section at
http://wiki.galaxyproject.org/Admin/Get%20Galaxy should have the user cd
into galaxy-dist before performing hg update stable.
Hi Michael,
Thanks for the correction,
No problem, glad it was helpful.
Dannon Baker wrote:
Thanks for the bug fix, (and for the reminder that it was still
sitting in the inbox, sorry about that). I've verified the fix as
well and pulled it into -central.
-Dannon
On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons
Hey all,
I've been trying to run a workflow on Galaxy, which basically attempts to
establish a correlation between the Chip-Chip, Polymerase binding and Dnase
Hypersensitivity data. The input would be these 3 files, I am initially
performing a liftover on the Chip-Chip data to convert from hg18
Hi Dannon,
I deleted the declaration to select2 in base.mako (line 42) and that fixed the
problem for now. (thanks to Ted for the tip!)
-Robert
On Jun 4, 2013, at 1:30 PM, Dannon Baker wrote:
Hey Robert,
Thanks for catching this; I'm working on getting a fix out (this affects
multiple
All,
I manage a cluster and have been asked to set up a local instance of galaxy.
I'm neither a galaxy user nor a biologist, so apologies in advance if my
terminology is off.
I have a basic setup running now, but have been asked to include the option to
display at UCSC Main when a user
That'll work, but it'll deactivate select2 across the board for all pages
in your galaxy instance. I committed a fix for those specific admin pages
yesterday, available in galaxy-central (stable as well as default branch).
-Dannon
On Thu, Jun 6, 2013 at 1:37 PM, Robert Baertsch
Ah, I see it now.
https://bitbucket.org/galaxy/galaxy-central/commits/c4096b030f10eb346b24da98ce16b72d23672f03
On Jun 6, 2013, at 10:42 AM, Dannon Baker wrote:
That'll work, but it'll deactivate select2 across the board for all pages in
your galaxy instance. I committed a fix for those
I looked through others' problems, but this seems unique. I just did a
clean install of Ubuntu 12.04 and wanted to add Galaxy to integrate our
various pipelines (16S rRNA via qiime, RADseq data, small genome
assemblies). However, I seem to be stuck at the beginning of the install.
Followed
How did you install your python, or are you using the default ubuntu 12.04
version? The bz2 module should be distributed with any python since 2.3.
-Dannon
On Thu, Jun 6, 2013 at 3:25 PM, Andrew Krohn alk...@nau.edu wrote:
I looked through others' problems, but this seems unique. I just did
I am using the default ubuntu 12.04 python.
Andrew Krohn
PhD Candidate, NAU Biological Sciences
Research Technician, EnGGen
On Thu, Jun 6, 2013 at 1:17 PM, Dannon Baker dannon.ba...@gmail.com wrote:
How did you install your python, or are you using the default ubuntu 12.04
version? The bz2
For whatever reason, it looks like your python was compiled without bz2
support. The following links may help you get a usable python installed:
http://stackoverflow.com/questions/12806122/missing-python-bz2-module
Hi Linda,
Sorry I wasn't clear before. The fix for that first issue is in
galaxy-central's stable branch, which will be migrated to galaxy-dist
probably sometime next week. You can always pull directly from -central
though, using 'hg pull -u -b stable
Hi Ira,
is it still working for you?
I installed one repository in a fresh installation and executed:
export
GALAXY_TOOL_DEPENDENCY_DIR=/home/bag/projects/galaxy/galaxy-central/tool_deps/
; sh run_functional_tests.sh -installed
It failed with:
Failed to resolve dependency on 'SCRIPT_PATH',
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