Gatk2 Galaxy Wrapper Available, Testing And Help Needed

Question: Gatk2 Galaxy Wrapper Available, Testing And Help Needed

4.9 years ago by

Germany

Bjoern Gruening ♦ 5.1k wrote:

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 have done it as easy as possible to plugin your local installed version. Furthermore, we made it easy to disable the 'call home feature' of GATK2 (if you have a GATK keyfile). Read more about it: https://github.com/bgruening/galaxytools/blob/master/gatk2/readme.rst The code is stored here: https://github.com/bgruening/galaxytools/tree/master/gatk2 The ToolShed wrappers can be found here: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2 I would like to thank Jim Johnson, Nicola Soranzo, Dan Blankenberg and the Galaxy Team. If you like the wrappers you know what to do during the next GCC! If you have feedback or patches please let us know. Thanks, Bjoern

galaxy • 1.6k views

ADD COMMENT • link •

modified 3.7 years ago by philippe.moncuquet • 10 • written 4.9 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjorn

I'm not sure whether you are aware of this but GATK2 doesn't automatically create the fasta index file and the picard index doc file like the old gatk-1.4 did.

I'm wondering if you can modify the wrapper to create these files on the fly. I guess it would require the addition of either dependencies or binaries within the GATK2 package. (I guess the alternative would be to remove the history option from the "Choose the source for the reference" - but that would make me sad).

The issue is that if I want to bring my own fasta file as a reference and then use GATK2 tools I can select my fasta in the "Choose the source for the reference" menu item but the tool will always fail.

I run a public galaxy instance (galaxy-qld) and users coming with unsupported genomes are begging me for a fix (things like H37Rv TB genome for example). I understand when you run your own galaxy you can easily add a loc file but its just not possible for us to do this.

BTW please to hesitate to let me know if I'm mistaken about the above. :-)

Kind regards

Derek Benson

ADD REPLY • link written 3.5 years ago by d.benson • 0

Hi Derek,

we have a few tests in our wrappers that works with FASTA input. Can you tell me exactly which tools your are referring to?

The wrapper are hosted here: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2

Thanks,

Bjoern

ADD REPLY • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern Thanks for getting back to me. The realigner target creator was the specific tool. We had installed version 0.0.7 of the wrapper. Kind regards Derek

ADD REPLY • link written 3.5 years ago by d.benson • 0

Uhh, this is a pretty old version. Can you update them? This tool has a test case, so I think this worked before with a fasta file as reference https://github.com/galaxyproject/tools-iuc/blob/master/tools/gatk2/indel_realigner.xml

ADD REPLY • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k

3.7 years ago by

philippe.moncuquet • 10

Australia

philippe.moncuquet • 10 wrote:

Hi Bjoern,

I am trying to install GATK2 on my instance of Galaxy. I have installed binaries, then wrappers you developed.

During first phase of testing, tools were complaining about JAVA_VAR_PATH being not properly set. I hard coded it in the .bashrc of my galaxyuser. I am not sure it is the best practice but at least tools seems to work.

To test the installation, I ran ReduceReads. I got an error message about the fact that it was deprecated

##### ERROR MESSAGE: Walker ReduceReads is no longer available in the GATK; it has been deprecated since version 3.0 (use recommended best practices pipeline with the HaplotypeCaller)

I was wondering what was the rational of having this wrapper around (backward reproducibility?). I guess I am doing something wrong...any thoughts.

Thanks for the great work,

Philip

ADD COMMENT • link written 3.7 years ago by philippe.moncuquet • 10

Hi Philip,

you need to use GATK2.8, sorry. Our wrappers only support 2.8 at the moment. The license is somehow strange from GATK so we are not allowed to ship the JAR file and install GATK for you. You need to get this file and place it somewhere on your host. In a next step you should edit the file "$GALAXY_TOOL_PATH"/environment_settings/GATK2_PATH/iuc/gatk2/some_number/env.sh file and point to your JAR file location.

Hope this get's you started otherwise drop me a mail,

Ciao,

Bjoern

ADD REPLY • link written 3.7 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjorn,

Thanks for the help. I have installed version 2.8

galaxydev@galaxy-compute$ java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" --version 2.8-1-g932cd3a

I still get the same error in Galaxy about deprecation

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.3-0-g37228af): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Walker ReduceReads is no longer available in the GATK; it has been deprecated since version 3.0 (use recommended best practices pipeline with the HaplotypeCaller)
##### ERROR ------------------------------------------------------------------------------------------

The weird thing is that the error says that the version use is 3.3.0 when I am sure that the 2.8.1 is used. When I copy the command line executed by galaxy and execute it in the shell, it shows no error and execution seems to be fine.

galaxydev@galaxy-compute:/data/home/mon13m$ python /data/galaxyTools/shed_tools_dev/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/84584664264c/gatk2/gatk2_wrapper.py --stdout "/data/galaxyTools/galaxydev/database/files/009/dataset_9700.dat" -d "-I" "/data/galaxyTools/galaxydev/database/files/009/dataset_9685.dat" "bam" "gatk_input" -d "" "/data/galaxyTools/galaxydev/database/files/_metadata_files/000/metadata_123.dat" "bam_index" "gatk_input" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "ReduceReads" -o "/data/galaxyTools/galaxydev/database/files/009/dataset_9699.dat" $GATK2_SITE_OPTIONS --num_cpu_threads_per_data_thread 1 --disable_bam_indexing ' -d "-R" "/data/galaxyTools/galaxydev/database/files/009/dataset_9623.dat" "fasta" "gatk_input"
galaxydev@galaxy-compute:/data/home/mon13m$

I am a bit lost here, any suggestions would be appreciated.

Regards,

Philip

ADD REPLY • link written 3.7 years ago by philippe.moncuquet • 10

Have you changed your env.sh file to point to the new (old) 2.8 version? Galaxy picks up the wrong GATK version and this is usually defined in your env.sh file.

ADD REPLY • link written 3.7 years ago by Bjoern Gruening ♦ 5.1k

I can't believe missed that. I owe a beer, are you coming to GCC2015, if so I will see you there. Do you have any workflows that you use to test the installation ? I am still having problem to make genome references available but everything else seems to be working fine. Thanks for all the help.

ADD REPLY • link written 3.7 years ago by philippe.moncuquet • 10

I just realized that for reference genome to be added in gatk2, an entry at to be created for that specific .loc files in the tool_data_table_conf.xml file.

ADD REPLY • link written 3.5 years ago by Philipe Moncuquet • 40

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