Mercurial > repos > jjohnson > gatk2
view tool_dependencies.xml @ 1:9b8e2a158073 draft
Fix typo in unified_genotyper.xml, add dir path in tool_dependencies.xml
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 01 Nov 2012 13:44:41 -0500 |
parents | 74c05070a3f8 |
children | a65944bad5c1 |
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<?xml version="1.0"?> <tool_dependency> <package name="gatk" version="2.2"> <install version="1.0"> <actions> <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-latest.tar.bz2</action> <!-- this expands into GenomeAnalysisTKLite-2.2-2-gd3f5a5e/ which common_util.py tar_extraction_directory() does not find so the move file must contain the GenomeAnalysisTKLite-2.2-2-gd3f5a5e dir path --> <action type="move_file"> <source>GenomeAnalysisTKLite-2.2-2-gd3f5a5e/GenomeAnalysisTKLite.jar</source> <destination>$INSTALL_DIR/GenomeAnalysisTK.jar</destination> </action> <action type="set_environment"> <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable> </action> <action type="set_environment"> <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD</environment_variable> </action> </actions> </install> <readme> The following GATK2 analysis types require a License for commercial use and the full GATK2 build will need to be manually installed: haplotypecaller HaplotypeCaller Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. HaplotypeResolver Haplotype-based resolution of variants in 2 different eval files. reducereads CompareBAM Given two BAMs with different read groups, it compares them based on ReduceReads metrics. ReduceReads Reduces the BAM file using read based compression that keeps only essential information for variant calling See: http://www.appistry.com/gatk/gatk-faqs-static for Licensing details. The full GATK build can be acquired from: http://www.broadinstitute.org/gatk/download and GenomeAnalysisTK.jar need to be manually installed into the GATK2_PATH set for the GenomeAnalysisTKLite.jar The GATK2_SITE_OPTIONS environment variable can be modified in the env.sh in the tool_dependencies path can be modified for the local installation. </readme> </package> <package name="samtools" version="0.1.18"> <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> <action type="shell_command">make</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>misc/maq2sam-long</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Compiling SAMtools requires the ncurses and zlib development libraries. </readme> </package> </tool_dependency>