[galaxy-dev] GATK problem on Galaxy

Hi All, I am having problems using GATK Indel Realigner. We installed our own galaxy instance on a VM server and configured it to submit jobs through DRMAA to the clusters. The first error I got is: " ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file.

Re: [galaxy-dev] GATK 3.1

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

Re: [galaxy-dev] GATK 3.1

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

[galaxy-dev] GATK 3.1

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

[galaxy-dev] GATK - Depth of Coverage Error

Hi Everyone, Recently, I tried to use GATK - Depth of Coverage tool with my own .bam file on Galaxy for the first time. However it gave following error for each output. (see screenshot) > Depth of Coverage on data 4 and data 1 (output cumulative coverage > proportions sample) > error: > An err

Re: [galaxy-dev] GATK

t;How to obtain and use a GATK key" >> >> Or by pass it by removing the -et "NO_ET" line from the xml files. >> >> >> >> [image: Inactive hide details for sridhar srinivasan ---06/06/2013 >> 06:30:48 AM---Dear Developers, I am running GATK for

[galaxy-dev] GATK fasta file missing ERROR

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

[galaxy-dev] GATK DepthofCoverage tool

Hi Galaxy, When I try to process my exome data bam files using DepthOfCoverage under GATK tools (on the main instance), the program seems to keep running forever without ever completing. There is no error message output but the program never ends after going for several days! Could it be som

Re: [galaxy-dev] GATK tools not showing up in cloudman Galaxy installation

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: > >

Re: [galaxy-dev] GATK tools not showing up in cloudman Galaxy installation

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

[galaxy-dev] GATK fasta file not found ERROR

Dear Developers, I am using GATK for first time. I am doing Targeted reseq Analysis. while i am running Unified Genotyper in Galaxy interface. it gives error message as mentioned below.. "ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does not exist." But i places the Fasta f

Re: [galaxy-dev] GATK

for first time. In galaxy i use Unified Genotyper. I am > > From: sridhar srinivasan > To: Galaxy Dev > Date: 06/06/2013 06:30 AM > Subject: [galaxy-dev] GATK > Sent by: galaxy-dev-boun...@lists.bx.psu.edu > -- > > > > Dear Developers, >

Re: [galaxy-dev] GATK

xml files. From: sridhar srinivasan To: Galaxy Dev Date: 06/06/2013 06:30 AM Subject: [galaxy-dev] GATK Sent by:galaxy-dev-boun...@lists.bx.psu.edu Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below men

[galaxy-dev] GATK

Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below mentioned. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):

[galaxy-dev] GATK tools / Realigner Target Creator / pb to create java virtual machine

Hello, When we run "Realigner Target Creator for use in local realignment" , I have this error : *Dataset 19: Realigner Target Creator on data 5, data 6, and data 4 (GATK intervals)* Tool e

Re: [galaxy-dev] gatk lite

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

[galaxy-dev] gatk lite

Hello Is it possible to redirect the GATK tools in my local installation of Galaxy to use GATK Lite (which is free) rather than GATK. If so what files would need to be altered and how? I'm particularly interested in getting the "Depth of Coverage" tool to work. Thanks much Mark This mes

[galaxy-dev] GATK fails to create Java Virtual Machine

Hi Folks, I received an email from one of my end users that she was having an issue with the "Realigner Target Creator" under NGS: GATK Tools. Here's the error: An error occurred running this job: "Unable to access jar file /hpcdata/galaxy-setup/galaxy-dist/tool-data/shared/jars/gatk/GenomeA

Re: [galaxy-dev] GATK v2.x

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

[galaxy-dev] GATK v2.x

Is anyone working on adapting the GATK tools for a more recent version of GATK? The distributed version is 1.4, and GATK is up to 2.1. David Hoover Helix Systems Staff ___ Please keep all replies on the list by using "reply all" in your mai

[galaxy-dev] GATK Unified Genotyper Error

Hello all, one of my users encounters a strange error with the GATK tool "Unified Genotyper". At the end of the message you see the original error report. The problem there was that the reference genome is missing. The tool was run as a part of a bigger workflow, but I double checked the workfl

Re: [galaxy-dev] GATK tools

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

[galaxy-dev] GATK tools

Hello, One of our users has been using the GATK (beta) tools on the main instance of galaxy and would like to have them locally accessible. I have looked at the main toolshed but I couldn't find them there. Is there a place I can download the GATK files and xml files? -Rob ___

Re: [galaxy-dev] GATK Depth of Coverage error

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.

[galaxy-dev] GATK Depth of Coverage error

I am trying to run GATK's DepthOFCoverage using intervals and get the following error: failure preparing job Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 59, in run_job job_wrapper.prepare() File "/home/galaxy/galaxy-dist/lib/

Re: [galaxy-dev] GATK metadata problems

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

[galaxy-dev] GATK metadata problems

When I try to run a GATK analysis that uses a bam file as input, I get the following error in the html page: Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue. when the input file is a bam file that has not run yet or is still run

Re: [galaxy-dev] GATK / R local install configuration

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

Re: [galaxy-dev] GATK / R local install configuration

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

[galaxy-dev] GATK / R local install configuration

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 on my instance, as this tool is failing with this error: mv: /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat.pdf: No such

Re: [galaxy-dev] GATK unified genotyper

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

Re: [galaxy-dev] GATK unified genotyper

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

Re: [galaxy-dev] GATK Unified Genotyper

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

Re: [galaxy-dev] GATK Unified Genotyper

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

Re: [galaxy-dev] GATK Unified Genotyper

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

Re: [galaxy-dev] GATK Unified Genotyper

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

[galaxy-dev] GATK integration

Hey, I know, the GATK-tools is considered to be in alpha status, but maybe someone can help me. First, is there a documentation on which dependencies where to put (just to confirm I've done it correctly) ? Second, when I run the unified genotyper, I get the following error: [Wed May 25 15:57:04