Hi Team,
I am sorry to be a pest, but I am under-the-gun to get this resolved. I have
followed the instructions for installing GATK2 on my cloud VM. After doing
that I discovered that the version of java running on the VM was v1.6.x and
GATK2 required v1.7.0x. I removed version 6 and
First guess is that perhaps the system is still defaulting to using java 1.6
and not 1.7. What happens if you run “java -version” as the Galaxy system user?
Perhaps try a reboot of the vm as well to make sure that the Galaxy app is
running with java 1.7.
Also, is this a custom vm? If it using
@lists.bx.psu.edu
galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GATK2 java version related issues
First guess is that perhaps the system is still defaulting to using java 1.6
and not 1.7. What happens if you run “java -version” as the Galaxy system user?
Perhaps try
Hi Team,
I have installed GATK2 into a galaxy cloud instance to use the Unified
Genotyper for our sequencing course. However, when I run the tool I get the
following error message:
Dataset 41: Unified Genotyper on data 8 and data 13 (VCF)
Tool execution generated the following error message:
Hi,
I installed the GATK2 wrapper from iuc on the lastest galaxy version. It
fails to create the GATK2_PATH and GATK2_SITE_OPTIONS structures under
the /tool_dependency_dir/environment_settings/ location, without a clear
error (says 'never installed').
If I create the files manually, I can
Hello Geert,
This issue was corrected yesterday in change sets
https://bitbucket.org/galaxy/galaxy-central/commits/96fdb9168f28b2ffa463195d084c9278efb2465a
and
https://bitbucket.org/galaxy/galaxy-central/commits/58a057a02b896ae6d32571f7141f46ccb9006e54,
which are currently available in both
Hi Geert,
Hi,
I'm using the GATK2 tools from IUC, taken from the main toolshed. After
configuration, I'm able to run the tools as standalone jobs, and
everything works.
When I add the job to a workflow, The 'Using reference genome' selection
is empty (see screenshot in attachment for
Dear All,
I installed gatk2 from tool_shed, and see below for my
gatk2_picard_index.loc
Anyone can tell me what the mistake is? Old gatk can use this file to find
all reference genomes, but gatk2 cannot.
Fenglou
gatk2_picard_index.loc
Description: Binary data
Hi Fenglou,
which file have you edited? Under tool-data or
tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/340633249b3d/gatk2_picard_index.loc
?
Cheers,
Bjoern
Am 26.02.2014 22:37, schrieb Fenglou Mao:
Dear All,
I installed gatk2 from tool_shed, and see below for my
Thanks, edited the wrong file.
Fenglou
On 26 February 2014 16:40, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Fenglou,
which file have you edited? Under tool-data or tool-data/
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/340633249b3d/gatk2_picard_index.loc?
Cheers,
Bjoern
Am
No problem, your welcome.
If you have any other feedback, please get in touch!
Bjoern
Am 26.02.2014 23:59, schrieb Fenglou Mao:
Thanks, edited the wrong file.
Fenglou
On 26 February 2014 16:40, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Fenglou,
which file have you edited? Under
Hi,
I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here.
I've run into the following error:
# ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does
not exist.
I see via much googling that this error is due to a user input problem. I've
tried
Hi,
do you have access to the generated commandline from Galaxy and can
paste it her?
I’ve installed the latest version (using GATK2.8-1) of the GATK2
wrapper here. I’ve run into the following error:
# ERROR MESSAGE: The fasta file you specified
(/tmp/tmp-gatk-V7IrBw) does not
Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 12:26 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GATK2
Hi,
do you have access to the generated commandline from Galaxy and can paste it
her?
I’ve installed
/packages/galaxy/galaxy-dist/database/pbs/101.ec
Thanks,
-Sheldon
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 12:26 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GATK2
Hi,
do
-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GATK2
Hi Sheldon,
The loc file is tabular. I put the 2bit file in the directory and had
no success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED=1
if [ -n $SLURM_JOB_NUM_NODES
Hi all,
over the last month we developed a new version of GATK2 wrappers and are
now seeking for testers, users and overall feedback.
We are currently targeting GATK 2.8. One of the big issues with GATK2 is
the new licence. Because of that we can't install GATK2 with the
wrappers, but we hope we
17 matches
Mail list logo
