view tool_dependencies.xml @ 12:b40671bc73d5 draft

Add help to HaplotypeCaller

<?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-2.2-3-g63dddfb/
                     which common_util.py tar_extraction_directory() does not find
                     so the move file must contain the GenomeAnalysisTKLite-2.2-3-g63dddfb dir path
                 -->
                <action type="move_file">
                    <source>GenomeAnalysisTKLite-2.2-3-g63dddfb/GenomeAnalysisTKLite.jar</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="shell_command">ln -s GenomeAnalysisTKLite.jar GenomeAnalysisTK.jar</action>
                <action type="move_file">
                    <source>GenomeAnalysisTK.jar</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <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>