Hi Greg,
Thanks ... that's great. It's all working now.
Ira
On 04/05/2012, at 3:41 AM, Greg Von Kuster wrote:
> Hi Ira,
>
> Sample fiel handling for installed tool shed repositories was restricted to
> .loc.sample files as you discovered. I've enhanced this feature to copy all
> appropria
Hi all,
Do the uploaded files in Galaxy get indexed or sorted already?
Cheers,
CL
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This is my code for running samtools pileup:
open INP,"< $ARGV[0]"
or die "Cannot open file! $!";
open INP2, "< $ARGV[1]"
or die "Cannot open file! $!";
open OUT,"> $ARGV[2]"
or die "Cannot open file! $!";
open SCRIPT,"samtools pileup -cv -f $ARGV[0] $ARGV[1] 2>/dev/null | ";
while(
I have had Galaxy running on a local BAS, and after success with that we're
ready to create an instance on our local cluster computing service. The local
cluster uses PBS/Torque.
I'm familiar with the basics of configuration, but our particular scheduler
rewards those who specify accurate wallt
Liisa,
Are there any errors in your paster.log or javascript console? What revision
are you running?
-Dannon
On May 3, 2012, at 2:28 PM, Liisa Koski wrote:
> Hello,
> I cloned a workflow on my local Galaxy installation, renamed it, made some
> edits and pressed save. It has been saving now
Dear all,
I have a local installation of Galaxy.
I need to create a new galaxy tool.
My python program runs outside Galaxy. When I call it through Galaxy it
does not find my custom libraries.
*
*
*ImportError: No module named NSISSoft.NSISBase*
*
*
*I understand it is a PYTHONPATH problem. How can
Hello,
I cloned a workflow on my local Galaxy installation, renamed it, made some
edits and pressed save. It has been saving now for about 3 hours. It only
has 12 steps.
Any suggestions?
Thanks in advance,
Liisa
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Hi Ira,
Sample fiel handling for installed tool shed repositories was restricted to
.loc.sample files as you discovered. I've enhanced this feature to copy all
appropriate .sample files contained in the installed repository to the
tool-data directory of the Galaxy instance to which the reposit
+1. This is especially useful for us, with hardware-accelerated
algorithms having limits on input size.
On 12-05-03 9:51 AM, "Peter Cock" wrote:
>Hello all,
>
>Currently the Galaxy experimental task splitting code allows splitting
>into
>N chunks, e.g. 8 parts, with:
>
>..." />
>
>Or, into c
Hi,
I regularly use "NGS: SAM Tools/Filter SAM" tool. Filtering after
mapping with BWA is a required step. I feel my current approach to
reintroduce the header after filtering is very wasteful. Wouldn't be
great if this tool had an option to keep the header? This sounds
simple enough. In fact look
Hello all,
Currently the Galaxy experimental task splitting code allows splitting into
N chunks, e.g. 8 parts, with:
Or, into chunks of at most size N (units dependent on the file type, e.g. lines
in a tabular file or number of sequences in FASTA/FASTQ), e.g. at most 1000
sequences:
As an as
On Thu, May 3, 2012 at 3:54 PM, Dannon Baker wrote:
>> On a related point, I've noticed sometimes one child job from a split task
>> can fail, yet the rest of the child jobs continue to run on the cluster
>> wasting
>> CPU time. As soon as one child job dies (assuming there are no plans for
>> at
> On a related point, I've noticed sometimes one child job from a split task
> can fail, yet the rest of the child jobs continue to run on the cluster
> wasting
> CPU time. As soon as one child job dies (assuming there are no plans for
> attempting a retry), I would like the parent task to kill al
On Tue, May 1, 2012 at 3:46 PM, Dannon Baker wrote:
> I'll take care of it. Thanks for reminding me about the TODO!
>
On a related point, I've noticed sometimes one child job from a split task
can fail, yet the rest of the child jobs continue to run on the cluster wasting
CPU time. As soon as on
Also, this issue with uploading Cuffmerge files to Galaxy Cloudman is
specific to Cuffmerge files I have generated within the last ~24 hours (on
Galaxy Main). I can upload these same files to main Galaxy server with no
problem. It is specific to Galaxy Cloudman.
Thanks for any help!
Cheers,
Mo H
Hello,
I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf
files just fine, but not the "merged transcripts.gtf" file from Cuffmerge.
This is the first time this has happened.
After I upload my "merged transcripts.gtf" file (via ftp) I can not move
the file to the history pa
On Thu, May 3, 2012 at 11:40 AM, Hans-Rudolf Hotz wrote:
> On 05/03/2012 12:10 PM, Peter Cock wrote:
>>
>> Hi all,
>>
>> Is it possible for a Galaxy Admin to browse any user's history?
>> Sadly the "Admin" page on the wiki is still rather lean:
>> http://wiki.g2.bx.psu.edu/Admin/Interface
>>
>> Fo
Hi,
Just to keep you updated of my progress. I've just been talking with our
cluster administrator, and they are going to install LSF client on the machine
which currently host our Galaxy server making it a submitting node to the
cluster. I am now waiting to test how it is going to work when al
Hi Dan and Greg,
Thanks for your answers on this. So far I have managed to make things work
following Dan's suggestion ... except that I can't seem to get my configuration
data file to install into tool-data. I'm not sure why this might be since all
my XXX.loc.sample files install into tool-
On 05/03/2012 12:10 PM, Peter Cock wrote:
Hi all,
Is it possible for a Galaxy Admin to browse any user's history?
Sadly the "Admin" page on the wiki is still rather lean:
http://wiki.g2.bx.psu.edu/Admin/Interface
For instance, I've monitored a large Galaxy job on our cluster, and now
that it
Hi Ira,
You'll need to include an entry for the display application in a
datatype_conf.xml file in the tool shed repository- this will result in the
display application being properly installed with the repository and made
functional in the local Galaxy instance. For details about this, see th
Hi all,
Is it possible for a Galaxy Admin to browse any user's history?
Sadly the "Admin" page on the wiki is still rather lean:
http://wiki.g2.bx.psu.edu/Admin/Interface
For instance, I've monitored a large Galaxy job on our cluster, and now
that it has finished I'd like to see the results (in t
Hi Guys,
After the most recent 'hg pull -u' followed by 'hg merge', I get the
following error in paster.log when I try to restart Galaxy:
galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,375 Loaded history export
tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2012-05-03 11:17:10,376 Loaded
Thanks Peter for your response!
Since I posted my question I also discovered that the header panel (aka
"masthead) is controled by the script
database/compiled_templates/webapps/galaxy/base_panels.mako.py
Best Regards,
Pascal
On Thu, May 3, 2012 at 10:16 AM, Peter Briggs wrote:
> Hi Pascal
>
>
Hi Pascal
I didn't see anyone else reply to this, but for our local Galaxy install
I use the "front page" in static/welcome.html as a place to put
information on usage policies and recent changes.
There are also some options in universe_wsgi.ini:
- "logo_url" sets the URL that’s linked from
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