Dear Developers,
I am GATK (beta ) Unified Genotyper module to get the indels and SNP.
I placed the jar file in (/galaxy-dist/tool-data/shared/jars/gatk) and i
link the reference genome in .loc file (gatk_sorted_picard_index.loc). I
could see the Name i mentioned in the .loc file is appearing in
Dear Developers,
I want to design a tool whose input is folder containing files and
sub-folders.
I was wandering which value should I assign to "TYPE" attribute of PARAM
tag in INPUTS.
--
Best regards,
Pankaj Narang
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Hi all,
A Cheetah question: when I enter ";" as a value in a text box of a tool
(stored in $exp), Cheetah prints this as "X", and passed this string to
the tool.
How to disable this behaviour in Cheetah? I have tried to play with
#filter directives, but to no avail.
Thanks,
Joachim
--
J
Hi Joachim,
try that one:
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
Cheers,
Bjoern
> Hi all,
>
>
> A Cheetah question: when I enter ";" as a value in a text box of a tool
> (stored in $exp), Cheetah prints this as "X", and passed this string to
> the
On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB |
wrote:
> Hi all,
>
>
> A Cheetah question: when I enter ";" as a value in a text box of a tool
> (stored in $exp), Cheetah prints this as "X", and passed this string to the
> tool.
>
> How to disable this behaviour in Cheetah? I have tried to
Hi everybody
Since yesterday all processes I have run on Galaxy main are waiting. The
system displayed a message to contact a Galaxy admin, but I could find no
other way rather than this mailing list.
Is this freeze due to a public maintenance, or it's just my problem?
Best wishes,
Ali
_
Hello Ladies and Gentlemen,
I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
have to setup Galaxy to find SNP's in genomes from hcc patients. I have a
64-bit openSuse 11.3 server on which I installed Galaxy locally, since we
have a) very large files (>30GB per patient) and
Thanks both of you! Okay, so I was looking in the wrong direction. This
solved the issue.
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 07/24/2013 11:13 AM, Björn Grüning wrote:
Hi Joachim,
try that one:
http://wiki.galaxyproject.org/Admin
Okay, normally I would have forked the galaxy-dist and do a pull request
with my change.
But the change I want to commit is in the tool 'add_value', which is in
the toolshed. Seems like a safer approach to me to contribute to the
toolshed. How can I commit my changes to that tool? Can somebody
Hi,
> Okay, normally I would have forked the galaxy-dist and do a pull request
> with my change.
>
> But the change I want to commit is in the tool 'add_value', which is in
> the toolshed. Seems like a safer approach to me to contribute to the
> toolshed. How can I commit my changes to that to
On Wed, Jul 24, 2013 at 11:25 AM, Björn Grüning
wrote:
> Hi,
>
>> Okay, normally I would have forked the galaxy-dist and do a pull request
>> with my change.
>>
>> But the change I want to commit is in the tool 'add_value', which is in
>> the toolshed. Seems like a safer approach to me to contribu
Hmm, seems that collaborating on tools is kind of a burden... Three
places to notify this small change you say? (trello, galaxy-dev and
direct emailing to the authors.)
I have opted for Trello, card #1013
Cheers,
J
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On Wed, Jul 24, 2013 at 1:56 PM, Joachim Jacob | VIB |
wrote:
> Hmm, seems that collaborating on tools is kind of a burden... Three places
> to notify this small change you say? (trello, galaxy-dev and direct emailing
> to the authors.)
>
> I have opted for Trello, card #1013
> Cheers,
https://tr
Peter,
Thank you for reporting this issue, it has been fixed in
10253:27b458743a11, and the test tool shed has been updated to that
revision.
--Dave B.
On 7/23/13 12:29:34.000, Peter Cock wrote:
On Tue, Jul 23, 2013 at 5:20 PM, Peter Cock wrote:
Hi Gred,
I'm trying to update this repo
Hi peter,
I've made this change in 10254:e22f360cda13, so now only those readme files
whose file anme ends in .rst will be rendered as such.
Thanks!
Greg Von kuster
On Jul 23, 2013, at 12:24 PM, Peter Cock wrote:
> On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster wrote:
>> Hello Björn,
>>
Hi James,
thanks for the short reply.
I have created a trello card. Here is the link
https://trello.com/c/SRxD991Y/1012-workflow-default-parameters
Feel free to vote.
Best regards, Jens
> -Ursprüngliche Nachricht-
> Von: ja...@taylorlab.org [mailto:ja...@taylorlab.org] Im Auftrag von
>
On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock wrote:
> On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster wrote:
>> Hello Björn,
>>
>> This one has been applied in changeset 10219:a7edac403b6c, and all of
>> your patches are now running on the test tool shed.
>>
>> Thanks very much,
>>
>> Greg Von Ku
What format are the files you are trying to process with MACS in?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 23, 2013 at 3:05 PM, Jianxin Wang wrote:
> Hi Galaxy dev team,
>
> I'm trying to the you galaxy server to do NGS peak calling: Tools -> NGS:
> Peak Ca
The cluster status log has the following:
* 14:49:00 - Setting up SGE...
* 14:49:09 - Postgres service prerequisites OK; starting the service
* 14:49:10 - PostgreSQL daemon NOT running.
* 14:49:10 - PostgreSQL daemon NOT running.
* 14:50:11 - ---> PROBLEM, running command '/b
Hi,
what is the relationship between workers defined in universe and job_conf.xml?
e.g.:
[server:handler0]
use = egg:Paste#http
port = 9092
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
a) do I have to specify the sum of the workers in job_conf.xml
Hi Moritz
I am not a galaxy tool shed expert, but I recommend you start with
reading these wiki pages:
http://wiki.galaxyproject.org/Tool%20Shed
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
and then try installing BWA via the tool shed and ask (if any) specific
questions (
use_threadpool and threadpool_workers specify the number of threads
for handling web requests and have nothing to do with job running.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir wrote:
> Hi,
>
> what is the relationship between
Ah yes,
this was local_job_queue_workers and cluster_job_queue_workers in universe.ini
thank you very much,
ido
On Jul 24, 2013, at 5:10 PM, James Taylor wrote:
> use_threadpool and threadpool_workers specify the number of threads
> for handling web requests and have nothing to do with job runn
Hi Gromobir,
The file that Gift is producing is already an html file and there's
already an html datatype in Galaxy by default. The output file in
question just invokes remote javascript libraries inside
The best contact address for these kinds of issues is galaxy-b...@bx.psu.edu
.
There was a brief delay with some jobs running, but everything should be
working fine now.
-Dannon
On Wed, Jul 24, 2013 at 5:30 AM, Ali Sharifi Zarchi wrote:
> Hi everybody
>
> Since yesterday all processes I have r
Shantanu,
I've yet been unable to reproduce this issue on a local installation of
a tool shed. If I do manage to reproduce it, I will re-open the issue
and find a fix.
--Dave B.
On 7/17/13 16:31:56.000, Greg Von Kuster wrote:
Hello Shantanu,
I've created a Trello card for this - we'll t
[Copying the list].
-Original Message-
From: , Srinivas Maddhi
Date: Wednesday, July 24, 2013 10:01 AM
To: "Perez, Ricardo"
Subject: Re: [galaxy-dev] Bowtie2 error: Creates a 62 kb file.
>Hi Ricardo,
>
>Ensuring that the appropriate reference indices are present, properly
>configured a
It would be very useful to know what's in the 62kb file -- is it a BAM file or
a long error message?
Also, the Bowtie2 wrapper has been updated in -central, so you may want to
check that out as well.
J.
On Jul 24, 2013, at 5:07 PM, Maddhi, Srinivas wrote:
> [Copying the list].
>
>
> -Or
You'll want to use composite datatypes:
http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
On Jul 24, 2013, at 3:08 AM, Pankaj Narang wrote:
> Dear Developers,
>
> I want to design a tool whose input is folder containing files and
> sub-folders.
> I was wandering which value s
Hi- there is a new problem: started 07/24/2013 21:16:27
./test_dependencies.sh
All required executables found in PATH
All required R packages are installed
Required module not found:
/mnt/galaxyData/custom/bin/python_libs/lib/python/pysam-0.6-py2.7-linux-x86_64.egg/csamtools.so:
undefined symbol:
Hello group,
I am trying to write lumi wrapper for Galaxy. Is anyone is writing or
already have written lumi wrapper for Galaxy. I couldn't find in both
galaxy main tool shed and test tool shed.
Regards
Sachit
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