Hi, I've seen there is a new version (3.1-1) of GATK available at http://www.broadinstitute.org/gatk/download . Are there any plans of getting this version into Galaxy in the nearer future? Greetings, Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner@jki.bund.de
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 for GATK v.2 on the Tool Shed: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2 which is developed and maintained by Jim Johnson, Björn Grüning and me. GATK v.3 has some new tools and also some changes to logging which prevent the use of gatk2 wrapper with v.3 , so we are planning to create a new gatk3 Tool Shed repository sooner or later, no time frame decided yet. You can follow development, and contribute if you want, at this git repository: https://github.com/bgruening/galaxytools Best, Nicola -- Nicola Soranzo, Ph.D. Bioinformatics Program, CRS4 Loc. Piscina Manna, 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/
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 available at http://www.broadinstitute.org/gatk/download . Are there any plans of getting this version into Galaxy in the nearer future?
Greetings, Thomas
---
Thomas Berner
Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany -
Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner@jki.bund.de
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participants (3)
-
Berner, Thomas -
Björn Grüning -
Nicola Soranzo