Hi Thomas,
we are have some rough plans to do that, as Nicolas already mentioned.
But at first we want to release one final GATK2.8 wrapper.
Help is very much appreciated.
Cheers,
Bjoern
Am 18.03.2014 14:41, schrieb Berner, Thomas:
Hi,
I've seen there is a new version (3.1-1) of GATK availa
Il 2014-03-18 14:41 Berner, Thomas ha scritto:
Hi,
I've seen there is a new version (3.1-1) of GATK available at
http://www.broadinstitute.org/gatk/download [1] .
Are there any plans of getting this version into Galaxy in the nearer
future?
Hi Thomas,
as you probably know there is a wrapper f
Thanks for the suggestin Linda...
i removed the line
-et "NO_ET" ##ET no phone home
Now i am not getting the Error as get key to run the GATK..
But i am getting error as the fasta file is not found..
even in backend i found the command as mentioned below
in the reference file section "-R " the
Hi Dan,
Thanks for the help. The Galaxy missing tools are now loaded and working as
expected.
Best regards,
Marco
On Thu, Jun 20, 2013 at 3:36 PM, Daniel Blankenberg wrote:
> Hi Marco,
>
> You'll need to enable some missing tool data tables in
> tool_data_table_conf.xml. i.e. adding:
>
>
Hi Marco,
You'll need to enable some missing tool data tables in
tool_data_table_conf.xml. i.e. adding:
value, dbkey, name, path
value, name, gatk_value, tools_valid_for
Also make sure the files exist at the listed , they probably
Hello Linda,
Thanks for your suggestions.
i removed the line from xml file but now i am getting different error.
# ERROR
--
# ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
# ERROR 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:
You could rename the file from "GenomeAnalysisTKLite.jar" to "GenomeAnalysisTK.jar" in the directory where you placed GATK...Something like/home/svcgalaxy/g/tool-data/shared/jars/gatkand it should work...ThonOn Jan 03, 2013, at 02:54 PM, mark.r...@syngenta.com wrote:Hello Is it possible to redirect
David, because of the restrictive licensing terms of GATK2 the main
Galaxy Team will not continue to develop any GATK tools except for
those which remain under the open source license (basically, GATK
1.6).
We will be very happy to have wrappers for these and other
non-open-source tools contribute
Hi Rob,
At this time, these tools are still included within the main Galaxy
distribution under tools/gatk. I would recommend using the latest version
available from galaxy-central until they are migrated into the toolshed.
Please let us know if you encounter any issues.
Thanks for using Gala
Hi Curt,
This should be fixed in -central (https://bitbucket.org/galaxy/galaxy-central)
in changeset 6778:35be930b21be and will be available in the next dist release.
If you don't want to wait until the next dist release, you can also pull
directly from central or apply the changes manually.
Hi Curt,
This is an annoyance when trying to use these tools interactively, but running
or designing a workflow in the editor should work just fine. The issue is that
for Galaxy the BAM index is technically considered an optional metadata
attribute, but it is required for GATK. I've removed the
Hi Carlos,
Are you using a version of GATK that is 1.3?
Another possibility is that you are missing an R library (e.g. 'ggplot2'), that
is used by the VariantRecalibrator for building the plots. Start up an
interactive R session and type: "library('ggplot2')"
If you are missing the library, t
Hi,
Any chances someone could give me hint on this issue?
Thanks in advance,
Carlos
On Tue, Nov 29, 2011 at 2:02 PM, Carlos Borroto
wrote:
> Hi,
>
> I'm testing the GATK pipeline and I ran into a problem with "Variant
> Recalibrator" tool. It seems I don't have correctly configure R and
> GATK
Hi Ilya,
Something similar to this is planned, but directly referencing location files
is being deprecated in favor of using the tool_data_tables mechanism. The
validator implementation does not yet support data tables, but will be enhanced
in the future. Additionally, the selection functional
To prevent user error in mixing genomes, would you be interested in a feature
in which the unified genotyper choses the genome in a fashion similar to how
samtools know which which genome to use?
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illum
Hi Ilya,
--genotype_likelihoods_model / -glm is available under advanced options for the
tool; it can be set to both, snp or indel. This parameter might be pulled out
from the advanced options heading and placed on the base options in the future
to make it easier to access. Thanks for the sugg
The newest version of the Unified Genotyper has a -glm option which needs to be
set to both to call indels.
BTW, any interest in writing a wrapper for the Depth of Coverage tool?
Thanks,
Ilya
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Wednesday, September 07, 2011 10:57 AM
To: Ch
Hi Ilya,
The JVM can be quite a pain when determining the best way to determine max
memory, however the underlying gatk_wrapper.py script was updated last week in
5970:20215fcf6da7 to allow using -Xmx or XX:DefaultMaxRAMFraction. Each of the
GATK tools are currently already set to use 'XX:Defau
Hi Daniel,
I have been implementing the GATK unified genotyper and I was having some
issues. Occasionally I would get an error that the Java virtual machine would
not start. I got around that by adding the Xmx3g parameter to the command line.
I also added the -nt 3 because otherwise it's really
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