SOFT : GATK
------
Site du soft: https://software.broadinstitute.org/gatk/
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LICENSE:
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-->  Version v3.8-0

FOR-PROFIT PURPOSES: If you plan to use GATK in any for-profit application, you are required to purchase a license. To do so, please contact softwarelicensing@broadinstitute.org to discuss your application with our license manager.
ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES: Under this license, you can use the program and view the source code for free as long as you are using GATK strictly for non-profit purposes. The full text of this license is included below. If your usage qualifies for this license, you can download the program and start using it right away.

https://software.broadinstitute.org/gatk/download/licensing

--> Version v4.0.0.0

Ffully open-source under a BSD 3-clause license: https://software.broadinstitute.org/gatk/download/licensing


See software documentation for more informations.

Location: /usr/local/bioinfo/src/GATK
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Load binaries and environment:
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-> Version v3.5

module load bioinfo/GATK-3.5
and
java -jar $GATK_HOME/GenomeAnalysisTK.jar -h or java -jar -classpath GenomeAnalysisTK.jar -h

or use absolute path:
java -jar /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar


-> Version 3.7

module load bioinfo/GATK-3.7
and 
java -jar $GATK_HOME/GenomeAnalysisTK.jar -h or java -jar -classpath GenomeAnalysisTK.jar -h

or use absolute path:
java -jar /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-3.7-0-gcfedb67/GenomeAnalysisTK.jar -h


-> Version v3.8-0

module load bioinfo/GATK-3.8-0
and
java -jar $GATK_HOME/GenomeAnalysisTK.jar -h or java -jar -classpath GenomeAnalysisTK.jar -h

or use absolute path:
java -jar /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar


-> Version 3.8-1-0

module load bioinfo/GATK-3.8-1-0
and 
java -jar $GATK_HOME/GenomeAnalysisTK.jar -h or java -jar -classpath GenomeAnalysisTK.jar -h

or use absolute path:
java -jar /usr/local/bioinfo/src/GATK/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar


-> Version v4.0.0.0

module load bioinfo/gatk-4.0.0.0

gatk --java-options "-Xmx4G" [program arguments]


-> Version v4.0.10.0

module load bioinfo/gatk-4.0.10.0

gatk --java-options "-Xmx4G" [program arguments]


-> Version v4.0.11.0

module load bioinfo/gatk-4.0.11.0

gatk --java-options "-Xmx4G" [program arguments]


-> Version v4.1.1.0

module load bioinfo/gatk-4.1.1.0

gatk --java-options "-Xmx4G" [program arguments]


-> Version v4.1.2.0

module load bioinfo/gatk-4.1.2.0

gatk --java-options "-Xmx4G" [program arguments]

-> version v4.1.7.0
module load bioinfo/gatk-4.1.7.0

gatk --java-options "-Xmx4G"


-> Version v4.1.9.0

module load bioinfo/gatk-4.1.9.0

gatk --java-options "-Xmx4G" [program arguments]


-> Version v4.2.0.0

module load bioinfo/gatk-4.2.0.0

gatk --java-options "-Xmx4G" [program arguments]


-> Version v4.2.2.0

module load bioinfo/gatk-4.2.2.0

gatk --java-options "-Xmx4G" [program arguments]

-> Version v4.2.6.1

module load bioinfo/gatk-4.2.6.1

gatk --java-options "-Xmx4G" [program arguments]


Example directory for use on cluster:
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/usr/local/bioinfo/src/GATK/example_on_cluster

To submit:
sbatch test_GATK-3.8-0.sh

or

sbatch test_GATK-4.0.0.0.sh
See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.