Hi David
Have you looked into the excellent Galaxy Unix-Tools package created
by Gordon Assaf?
http://hannonlab.cshl.edu/galaxy_unix_tools/index.html
The Find Replace text in line/column tool is probably what you are
looking for:
Hi all,
So far we've been running our local Galaxy instance on
a single machine, but I would like to be able to offload
(some) jobs onto our local SGE cluster. I've been reading
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
Unfortunately in our setup the SGE cluster head node
Hello everyone
I'm updating the remaining questions:
1) We use LDAP for user registration and logging, would it be possible
to retrieve automatically the LDAP users' groups and create the groups
in Galaxy accordigly? (and of course put the user in their respective
groups)
2) Is it possible,
On Tue, Apr 26, 2011 at 5:11 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
So far we've been running our local Galaxy instance on
a single machine, but I would like to be able to offload
(some) jobs onto our local SGE cluster. I've been reading
On Tue, Apr 26, 2011 at 12:10 PM, Sean Davis sdav...@mail.nih.gov wrote:
On Tue, Apr 26, 2011 at 5:11 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
So far we've been running our local Galaxy instance on
a single machine, but I would like to be able to offload
(some) jobs onto our
Does anybody have any idea why I would be getting this error before the
tool runs?
--
Branden Timm
Great Lakes Bioenergy Research Center
bt...@wisc.edu
On 4/19/2011 10:45 AM, Branden Timm wrote:
Hi All,
I'm having issues running BWA for Illumina with the latest version
of Galaxy
Hello Leon,
Are you still experiencing problems with your local install? Could you
confirm that you have attempted this again with the current distribution
(April 8th) and have completed the NGS Tool set up as described in our
wiki? Once we know everything is current it will be easier to
Hi Branden,
I find a wiki documentation here,
https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables
Hope this will help you to experiment a bit around.
regards, Vipin
Does anybody have any idea why I would be getting this error before the
tool runs?
--
Branden Timm
Great Lakes
After logging out and then using the back button, what is it that you're able
to do or that you're worried about? Any action on pages you click 'back' to
get to should now present a You must be logged in to Galaxy... error message.
To your question about disabling it, back button
You can certainly adjust the two values as needed for your particular
environment. Also check in your universe_wsgi.ini for:
set_metadata_externally = True
Something else you might want to consider, and what we do to handle the load on
the server at http://usegalaxy.org, is starting more
Hello all,
The 2011 Galaxy Community Conference registration site is now back online.
See http://galaxy.psu.edu/gcc2011/Register.html for details. Early
registration ends May 1.
*May 24 Lodging:*
As expected, we *were not able* to secure additional hotel rooms at the
conference centre for May
Hi Dannon,
Thanks for pointing the same.
Vipin,
The numerical portion of the file path is not saved in the database, rather
it is generated on the fly by the function directory_hash_id in
lib/galaxy/model/__init__.py. The filename itself should be named in the
format dataset_dataset
Vipin, thanks for the tip. I was not aware of data tables at all.
I checked bwa_wrapper.xml and it is still using the from_file attribute
for the reference genome parameter, not from_data_table. It would
appear then that BWA is not using data tables? Additionally, I have now
noticed that
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