Re: [galaxy-dev] GATK2 java version related issues
Hi Dan, I had suspected that, but when I run java –version I get the following: java version "1.7.0_65" OpenJDK Runtime Environment (IcedTea 2.5.1) (7u65-2.5.1-4ubuntu1~0.12.04.2) OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode) I have rebooted the VM and nothing has changed. The VM is built on AWS cloud and is using the latest galaxy ami: 1. AMI: ami-a7dbf6ce 2. Name: Galaxy CloudMan<https://wiki.galaxyproject.org/CloudMan> 2.3 The only difference is that I needed to upgrade the java version for GATK2 and snpEff. I currently have just a single node running so there is no issue with the wrong java version running on additional nodes. Thanks, Iry From: Daniel Blankenberg mailto:d...@bx.psu.edu>> Date: Friday, October 10, 2014 3:16 PM To: Iry Witham mailto:iry.wit...@jax.org>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" mailto: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 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 running things on different cluster nodes, you’ll need to make sure the java version on those nodes are 1.7 as well. Thanks, Dan On Oct 10, 2014, at 3:04 PM, Iry Witham mailto:iry.wit...@jax.org>> wrote: 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 installed version 7, uninstalled GATK2 and reinstalled it and reset all of the settings that may have reverted with the uninstalls/reinstalls. Now when I run Unified Genotyper I get the following error: Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:643) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) at java.net.URLClassLoader.access$000(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:212) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) Could not find the main class: org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit. Researching this I found a post at http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-tested-it-after-installing that refers to upgrading java as the solution. However, that did not fix the issue. In addition I copied the jar file to a temp directory and unzipped it to examine the MANAFEST.MF file for versioning issues. This is what I found: Manifest-Version: 1.0 Build-Jdk: 1.7.0_51 Built-By: gsa-engineering Created-By: Apache Maven Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK Archiver-Version: Plexus Archiver This tells me that there is something else causing the problem. Does anyone have an idea where to look now? Regards,Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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 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 running things on different cluster nodes, you’ll need to make sure the java version on those nodes are 1.7 as well. Thanks, Dan On Oct 10, 2014, at 3:04 PM, Iry Witham wrote: > 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 installed version 7, > uninstalled GATK2 and reinstalled it and reset all of the settings that may > have reverted with the uninstalls/reinstalls. Now when I run Unified > Genotyper I get the following error: > > Exception in thread "main" java.lang.UnsupportedClassVersionError: > org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor > version 51.0 > at java.lang.ClassLoader.defineClass1(Native Method) > at java.lang.ClassLoader.defineClass(ClassLoader.java:643) > at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) > at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) > at java.net.URLClassLoader.access$000(URLClassLoader.java:73) > at java.net.URLClassLoader$1.run(URLClassLoader.java:212) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:205) > at java.lang.ClassLoader.loadClass(ClassLoader.java:323) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) > at java.lang.ClassLoader.loadClass(ClassLoader.java:268) > Could not find the main class: > org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit. > > Researching this I found a post at > http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-tested-it-after-installing > that refers to upgrading java as the solution. However, that did not fix > the issue. In addition I copied the jar file to a temp directory and > unzipped it to examine the MANAFEST.MF file for versioning issues. This is > what I found: > > Manifest-Version: 1.0 > Build-Jdk: 1.7.0_51 > Built-By: gsa-engineering > Created-By: Apache Maven > Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK > Archiver-Version: Plexus Archiver > > This tells me that there is something else causing the problem. > Does anyone have an idea where to look now? > > Regards,Iry > The information in this email, including attachments, may be confidential and > is intended solely for the addressee(s). If you believe you received this > email by mistake, please notify the sender by return email as soon as > possible. > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] gatk2 wrapper issue
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 the default and stable branches of the galaxy-central repository. The fix will be automatically pushed to the galaxy-dist repository at some point, but I'm not sure when - I believe it will be some time today. If you are tracking the stable branch on the galaxy-central repository, you can: hg pull hg update stable If you are tracking the galaxy-dist repository, you can get the fix later today. Thanks for reporting this, and sorry for the inconvenience. Greg Von Kuster On Jun 4, 2014, at 6:25 AM, Geert Vandeweyer wrote: > 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 see them through : Admin - Manage > installed toolshed repos - gatk2 - missing tool dependencies - GATK2_PATH > If I click the hyperlink for GATK2_PATH here (this is the install missing > dependency page), I can expand and show the GATK2_PATH / env.sh file > > > > Still, running GATK2 tools (eg UG, gives me in the logs: > galaxy.jobs.handler INFO 2014-06-04 12:18:07,333 (78998) Job dispatched > galaxy.tools.deps WARNING 2014-06-04 12:18:07,928 Failed to resolve > dependency on 'gatk2', ignoring > galaxy.tools.deps WARNING 2014-06-04 12:18:07,971 Failed to resolve > dependency on 'GATK2_PATH', ignoring > galaxy.tools.deps WARNING 2014-06-04 12:18:07,974 Failed to resolve > dependency on 'GATK2_SITE_OPTIONS', ignoring > > and tool error: > Unable to access jarfile /GenomeAnalysisTK.jar > > For my mutect_wrapper in test.toolshed, which I initially copied from the > gatk2 wrapper, the exact same setup seems to work. > > Any help would be appreciated. > > Best, > > Geert > -- > > Geert Vandeweyer, Ph.D. > Department of Medical Genetics > University of Antwerp > Prins Boudewijnlaan 43 > 2650 Edegem > Belgium > Tel: +32 (0)3 275 97 56 > E-mail: geert.vandewe...@ua.ac.be > http://ua.ac.be/cognitivegenetics > http://www.linkedin.com/in/geertvandeweyer > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK2 (from IUC) Missing reference_genome selection
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 PrintReads tool). Just filling in the database key (hg19 in my case) allows the workflow to run correctly. When I noticed that the Unified Genotyper does not show this behaviour, I checked the XML files. After commenting out the following line (which is commented in Unified Genotyper by default) in the "Realigner Target Creator" tool, The selection drop-down menu showed correctly for RTC: So I assume that this filter is conflicting with the workflow editor somehow. Is this an issue on my site only, or is this a general bug? Its a general issue, and I think its also a bug. That filter step should ensure that the genome dbkey from vcf and bam are identical. But it seems that the workflow editor is not supporting it. I had a look at bowtie2 and it seems bowtie2 also do not use that filter. If you like you can fill a trello card with that issue and please a PR to: https://github.com/bgruening/galaxytools for the GATK tools. On a side note: i'd like to be able to set the java --max_jvm_heap value on a per-gatk-tool basis without directly editing the xml files, instead of using the default heap_fraction setting. Is this possible (yet) ? Editing the XML files caused the update of toolshed_packages to fail by launching interactive diff-merge tasks when updating from the website. No that is currently not supported, at least not for every single tool, you can do that for all GATK tools if you like. I think we have a trello card for that feature request. Please upvote it :) Thanks for using the GATK wrappers and reporting these issues. Bjoern Kind regards, Geert ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK2 is unable to find reference genomes
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 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 26.02.2014 22:37, schrieb Fenglou Mao: 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK2 is unable to find reference genomes
Thanks, edited the wrong file. Fenglou On 26 February 2014 16:40, Björn Grüning 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 26.02.2014 22:37, schrieb Fenglou Mao: > >> 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 >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK2 is unable to find reference genomes
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 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK2
Hi,
Thanks for your help. It turns out an extra carriage return snuck into the end
of the .loc file. Once I removed that everything worked.
-Sheldon
From: bjoern.gruen...@googlemail.com [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 2:05 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GATK2
I have no clue what is happening. Attached is my working *.loc flile.
See select-box is also filtered by the db-key of your dataset, but I think you
habe hg19 as dbkey, otherwise you would not see the hg19 in the select box.
There must be something wrong in you *.log file.
2014-01-30 Briand, Sheldon
mailto:sheldon.bri...@ssc-spc.gc.ca>>:
We do see hg19 in the reference genome box. We are using revision 8bcc13094767
of the GATK2 wrapper. The only line in the .loc file is the one listed in my
first email. I've put that line in both tool-data and
tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767<http://toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767>
loc files. We didn't see the reference genome hg19 until the loc file for the
repo was populated.
Thanks!
-Sheldon
-Original Message-
From: Björn Grüning
[mailto:bjoern.gruen...@gmail.com<mailto:bjoern.gruen...@gmail.com>]
Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-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 "$SLURM_JOB_NUM_NODES" ]; then
> GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
> GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
> GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
> GALAXY_SLOTS="1"
> unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
> if [ -n "$PYTHONPATH" ]; then
> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
> else
> PYTHONPATH="$GALAXY_LIB"
> fi
> export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> /gatk2/8bcc13094767/env.sh; PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
> nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
> PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
> /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py<http://x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py>
> --stdout "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat" -d "-I"
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input" -d ""
> "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input" -p ' java -jar
> "$GATK2_PATH/GenomeAnalysisTK.jar"-T "Rea
> lignerTargetCreator" -o
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"
> $GATK2_S
> ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads
> ${GALAXY_SLOTS:-4}
> -R ""
-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running the
latest revision? Do you see hg19 / hg18 in the select-box under
"using-reference genome"
Can you attach your gatk2_picard_index.loc?
Thanks,
Bjoern
>
> '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /softw
Re: [galaxy-dev] GATK2
I have no clue what is happening. Attached is my working *.loc flile.
See select-box is also filtered by the db-key of your dataset, but I think
you habe hg19 as dbkey, otherwise you would not see the hg19 in the select
box. There must be something wrong in you *.log file.
2014-01-30 Briand, Sheldon :
>
> We do see hg19 in the reference genome box. We are using revision
> 8bcc13094767 of the GATK2 wrapper. The only line in the .loc file is the
> one listed in my first email. I've put that line in both tool-data and
> tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files.
> We didn't see the reference genome hg19 until the loc file for the repo was
> populated.
>
> Thanks!
> -Sheldon
>
>
>
> -Original Message-
> From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
> Sent: Thursday, January 30, 2014 1:33 PM
> To: Briand, Sheldon
> Cc: galaxy-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 "$SLURM_JOB_NUM_NODES" ]; then
> > GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> > elif [ -n "$NSLOTS" ]; then
> > GALAXY_SLOTS="$NSLOTS"
> > elif [ -f "$PBS_NODEFILE" ]; then
> > GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
> > GALAXY_SLOTS="1"
> > unset GALAXY_SLOTS_CONFIGURED
> > fi
> >
> > export GALAXY_SLOTS
> > GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> > if [ "$GALAXY_LIB" != "None" ]; then
> > if [ -n "$PYTHONPATH" ]; then
> > PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
> > else
> > PYTHONPATH="$GALAXY_LIB"
> > fi
> > export PYTHONPATH
> > fi
> >
> > [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> > /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> > 00/101
> > PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> > ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> > /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> > /gatk2/8bcc13094767/env.sh; PACKAGE
> > _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> > ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> > /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> > s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> > PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
> > nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
> > PACKAGE_BASE; .
> > /software/packages/galaxy/galaxy-dist/dependancies/environment_
> > settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
> /software/packages/galaxy/shed_tools/toolshed.g2.b
> > x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py
> --stdout "/software/packages/galaxy/galaxy-dist/da
> > tabase/files/000/dataset_126.dat" -d "-I"
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> > dat" "bam" "gatk_input" -d ""
> "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> > data_19.dat" "bam_index" "gatk_input" -p ' java -jar
> "$GATK2_PATH/GenomeAnalysisTK.jar"-T "Rea
> > lignerTargetCreator" -o
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"
> $GATK2_S
> > ITE_OPTIONS --num_cpu_threads_per_data_thread 1
> --num_threads ${GALAXY_SLOTS:-4}
>
>
> > -R ""
>
> -> that is the error. Here needs to be your path to the fasta file. Can
> you point to me to Tool Shed Version you are using and are you running the
> latest revision? Do you see hg19 / hg18 in the select-box under
> "using-reference genome"
>
> Can you attach your gatk2_picard_index.loc?
>
> Thanks,
> Bjoern
>
> >
> > '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> > /software/packages/galaxy/galaxy-dist/set_metadata.sh
> > ./database/files
> > /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> > 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
> > /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> > /software
Re: [galaxy-dev] GATK2
We do see hg19 in the reference genome box. We are using revision 8bcc13094767
of the GATK2 wrapper. The only line in the .loc file is the one listed in my
first email. I've put that line in both tool-data and
tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files. We
didn't see the reference genome hg19 until the loc file for the repo was
populated.
Thanks!
-Sheldon
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: galaxy-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 "$SLURM_JOB_NUM_NODES" ]; then
> GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
> GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
> GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` else
> GALAXY_SLOTS="1"
> unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
> if [ -n "$PYTHONPATH" ]; then
> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
> else
> PYTHONPATH="$GALAXY_LIB"
> fi
> export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc cd
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
> ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
> /gatk2/8bcc13094767/env.sh; PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
> ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_setting
> s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
> nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
> PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
> /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout
> "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat" -d "-I"
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input" -d ""
> "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input" -p ' java -jar
> "$GATK2_PATH/GenomeAnalysisTK.jar"-T "Rea
> lignerTargetCreator" -o
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"
> $GATK2_S
> ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads
> ${GALAXY_SLOTS:-4}
> -R ""
-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running the
latest revision? Do you see hg19 / hg18 in the select-box under
"using-reference genome"
Can you attach your gatk2_picard_index.loc?
Thanks,
Bjoern
>
> '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/0
> 00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
> /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> /software/packages/
> galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
> /software/packages/galaxy/galaxy-dist/database
> /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1
> 02_DXIvP5,/software/packages/galaxy/galaxy-dis
> t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA
> ssociation_102_ifJAbu,/software/packages/galax
> y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist
> oryDatasetAssociation_102_Ie2O0C,/software/pac
> kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada
> ta_results_HistoryDatasetAssociation_102_xLNtK
> a,,/software/packages/galaxy/galax
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 "$SLURM_JOB_NUM_NODES" ]; then
> GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
> elif [ -n "$NSLOTS" ]; then
> GALAXY_SLOTS="$NSLOTS"
> elif [ -f "$PBS_NODEFILE" ]; then
> GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
> else
> GALAXY_SLOTS="1"
> unset GALAXY_SLOTS_CONFIGURED
> fi
>
> export GALAXY_SLOTS
> GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
> if [ "$GALAXY_LIB" != "None" ]; then
> if [ -n "$PYTHONPATH" ]; then
> PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
> else
> PYTHONPATH="$GALAXY_LIB"
> fi
> export PYTHONPATH
> fi
>
> [ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc
> cd
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767;
> export PACKA
> GE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767/env.sh;
> PACKAGE
> _BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bcc13094767;
> exp
> ort PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc
> c13094767/env.sh;
> PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_SITE_OP
> TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; .
> /software/packages/galaxy/galaxy-dist/dependancies/environment_
> settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
> /software/packages/galaxy/shed_tools/toolshed.g2.b
> x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout
> "/software/packages/galaxy/galaxy-dist/da
> tabase/files/000/dataset_126.dat" -d "-I"
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
> dat" "bam" "gatk_input" -d ""
> "/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
> data_19.dat" "bam_index" "gatk_input" -p ' java -jar
> "$GATK2_PATH/GenomeAnalysisTK.jar"-T "Rea
> lignerTargetCreator" -o
> "/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"
> $GATK2_S
> ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads
> ${GALAXY_SLOTS:-4}
> -R ""
-> that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running
the latest revision? Do you see hg19 / hg18 in the select-box under
"using-reference genome"
Can you attach your gatk2_picard_index.loc?
Thanks,
Bjoern
>
> '; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
> /software/packages/galaxy/galaxy-dist/set_metadata.sh
> ./database/files
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101
> . /software/packages/g
> alaxy/galaxy-dist/universe_wsgi.ini
> /software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
> /software/packages/
> galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
> /software/packages/galaxy/galaxy-dist/database
> /job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_102_DXIvP5,/software/packages/galaxy/galaxy-dis
> t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax
> y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac
> kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK
> a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso
> ciation_102__IZJ7Y
> /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD
> atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k
> wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/10
> 1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages/galaxy/galaxy-dist/database/job_working_direc
> tory/000/101/metadata_results_HistoryDatasetAssoci
Re: [galaxy-dev] GATK2
Hi Bjoern,
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 "$SLURM_JOB_NUM_NODES" ]; then
GALAXY_SLOTS="$SLURM_JOB_NUM_NODES"
elif [ -n "$NSLOTS" ]; then
GALAXY_SLOTS="$NSLOTS"
elif [ -f "$PBS_NODEFILE" ]; then
GALAXY_SLOTS=`wc -l < $PBS_NODEFILE`
else
GALAXY_SLOTS="1"
unset GALAXY_SLOTS_CONFIGURED
fi
export GALAXY_SLOTS
GALAXY_LIB="/software/packages/galaxy/galaxy-dist/lib"
if [ "$GALAXY_LIB" != "None" ]; then
if [ -n "$PYTHONPATH" ]; then
PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
else
PYTHONPATH="$GALAXY_LIB"
fi
export PYTHONPATH
fi
[ -f "/home/galaxy/.bashrc" ] && . /home/galaxy/.bashrc
cd /software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767;
export PACKA
GE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc/gatk2/8bcc13094767/env.sh;
PACKAGE
_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bcc13094767;
exp
ort PACKAGE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_PATH/iuc/gatk2/8bc
c13094767/env.sh;
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_settings/GATK2_SITE_OP
TIONS/iuc/gatk2/8bcc13094767; export PACKAGE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/environment_
settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
/software/packages/galaxy/shed_tools/toolshed.g2.b
x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py --stdout
"/software/packages/galaxy/galaxy-dist/da
tabase/files/000/dataset_126.dat" -d "-I"
"/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
dat" "bam" "gatk_input" -d ""
"/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
data_19.dat" "bam_index" "gatk_input" -p ' java -jar
"$GATK2_PATH/GenomeAnalysisTK.jar"-T "Rea
lignerTargetCreator" -o
"/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat"
$GATK2_S
ITE_OPTIONS --num_cpu_threads_per_data_thread 1 --num_threads
${GALAXY_SLOTS:-4} -R ""
'; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
/software/packages/galaxy/galaxy-dist/set_metadata.sh
./database/files
/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101 .
/software/packages/g
alaxy/galaxy-dist/universe_wsgi.ini
/software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX /software/packages/
galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
/software/packages/galaxy/galaxy-dist/database
/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_102_DXIvP5,/software/packages/galaxy/galaxy-dis
t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetAssociation_102_ifJAbu,/software/packages/galax
y/galaxy-dist/database/job_working_directory/000/101/metadata_out_HistoryDatasetAssociation_102_Ie2O0C,/software/pac
kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_results_HistoryDatasetAssociation_102_xLNtK
a,,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_override_HistoryDatasetAsso
ciation_102__IZJ7Y
/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_in_HistoryD
atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/101/metadata_k
wds_HistoryDatasetAssociation_103_1e5Jn2,/software/packages/galaxy/galaxy-dist/database/job_working_directory/000/10
1/metadata_out_HistoryDatasetAssociation_103_NNh80i,/software/packages/galaxy/galaxy-dist/database/job_working_direc
tory/000/101/metadata_results_HistoryDatasetAssociation_103_ZVuezG,,/software/packages/galaxy/galaxy-dist/database/j
ob_working_directory/000/101/metadata_override_HistoryDatasetAssociation_103_LFaURY;
sh -c "exit $return_code"
echo $? > /software/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 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:
>
> # ERRO
Re: [galaxy-dev] GATK2
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 exist. > > > > I see via much googling that this error is due to a user input > problem. I’ve tried pointing the gatk2_picard_index.loc file in > tool-data to the proper data files: > > hg19 hg19hg19/software/packages/galaxy/data/picard/hg19.fa That look ok, as far as every token is separated by a tabular. > > where the following files exist: > > hg19.dict > > hg19.fa > > hg19.fa.fai Can you put the 2bit file into the same folder? Cheers, Bjoern > > I’m using a torque setup. A bam file is being used as input. After > much trial and error I’ve been unable to figure out what I’m > missing. > > > > None of the solutions on google apply to my situation. > > > > Has anyone else run into this configuration problem and solved it? > > > > Thanks, > > -Sheldon > > > > Sheldon Briand > > NRC Research Computing Support Analyst > > Research Computing Support / Soutien Informartique a la Recherche > > Operations, Science Portfolio / Operations, Portefeuil des sciences > > SSC-NRC / SPC-CNRC > > Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford > > Halifax, NS B3H 3Z1 > > 902 426-1677 > > sheldon.bri...@ssc-spc.gc.ca > > > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
