Hi Bjoern,
I'm using the full GATK version 2.4-9-g532efad in galaxy.
Best,
Geert
On 11/19/2013 08:28 PM, Björn Grüning wrote:
Hi Geert,
thanks for the information. Are you running GATK-2.4 or GATK-Lite-2.4.
As far I know the lite version is deprecated.
JJ are your wrappers in
I pushed a copy of GATK2 from the testtoolshed to bitbucket:
https://bitbucket.org/jjohnson/gatk2
The existing tool dependency no longer makes sense with the current licensing
and access policies by Broad.
Also, much of the duplication in the individual tool wrappers could be moved to
Hi Cesar,
The easiest way to avoid module version conflicts is to use virtualenv to
set up a self-contained environment:
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment
--nate
On Tue, Nov 19, 2013 at 4:02 PM, Cesar Rodriguez
Hello all,
It is my recollection that under the Admin panel, Manage jobs
page, there used to be a toggle control to lock the submission
of new jobs. This was very helpful in preparation for scheduling
a system shutdown (e.g. for hardware or software updates).
However, I no longer see this option
Thanks Jim,
I cloned it under:
https://bitbucket.org/BjoernGruening/gatk2
and added macros.
If you agree I will try to do the following during the next week:
- add GALAXY_SLOTS
--num_threads | -nt will be \${GALAXY_SLOTS:-4} and
-nct / --num_cpu_threads_per_data_thread
Data transfer into Amazon's cloud is completely free. Data out is what
costs money. See http://aws.amazon.com/pricing_effective_july_2011/
What you're trying to do here would be loading data *into* amazon from our
main server at usegalaxy.org. I'm not sure what you're asking with the
second
On Wed, Nov 20, 2013 at 9:07 AM, Manisha Sapre msa...@nmdp.org wrote:
apologies if the second question was not framed properly, but it seems
there is a fee to share output datasets between nodes on same master
instance ?
No.
___
Please
Hi all,
I recently tried uploading an couple of xml files to my
local Galaxy installation using the standard ‘Upload File (version 1.1.3)’
tool. For some files this produced the error: The uploaded file contains
inappropriate HTML content.
Given the files had been created by the same
Bjoern,
Looks good.
This page also had some info on per tool use of -nt and -nct
http://www.broadinstitute.org/gatk/guide/tagged?tag=nct
If remember correctly, GATK doesn't ignore options that don't apply, it just
does an ungraceful exit.
I not sure if I had that sorted out when I last
On Mon, Nov 11, 2013 at 5:29 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Nov 7, 2013 at 4:51 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Michiel,
Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...
If not, I may tackle this shortly.
Peter
I've
I'm doing a 1 step generic reporting tool along the lines of the BLAST XML to
tabular script by Peter. I was just about to ask about this line, which
looked pretty much like a bug:
sallseqid = ;.join(name.split(None,1)[0] for name in hit_def.split(
))
Then I found the patch from Nov
Woops - I realize now findtext() must be unescaping all gt;, so Peter was
trying to address other non-splitting occurances of as per his patch
notes. But perhaps a stop_err() isn't merrited in this case?
So ignore my test for gt; comment.
Regards,
Damion
Good Morning Dannon
this may not be a cost effective way of sharing data, cloud amazon charges
$0.120 per GB data transfer, is there a work around ?
also does that mean a worker node cannot communicate with master instance
directly and use same below protocol to share history ?
Thanks
msapre
data process and output is both on amazon ( input is free but storage and
transfer costs $)
the main server usegalaxy.orghttp://usegalaxy.org is only used to cross
check results of data running parallel on amazon for now.
apologies if the second question was not framed properly, but it seems
Hi Jim,
latest changes here:
https://bitbucket.org/BjoernGruening/gatk2
- more use of macros
- new tool_dependencies that just sets the GATK2_PATH and
GATK2_SITE_OPTIONS
- added GALAXY_SLOTS to all tools
- changes some inconsistency in loc file naming
This page also had some info on per tool
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