Mercurial > repos > jason-ellul > calculatezprimefactor
view tool_dependencies.xml @ 4:796653c6376b draft
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author | jason-ellul |
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date | Wed, 01 Jun 2016 02:36:11 -0400 |
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<?xml version="1.0"?> <tool_dependency> <!-- Optimized samtools (for threaded mpileup) <package name="samtools-parallel-mpileup" version="0.1.19"> <install version="1.0"> <actions> <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup && cd samtools-parallel-mpileup && cd $(ls |grep samtools-) && make && cp samtools ../samtools-parallel-mpileup</action> <action type="move_file"> <source>samtools-parallel-mpileup</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> Downloads and installs a modified version of samtools, able to paralellize the mpileup function. </readme> </package> --> <package name="samtools" version="0.1.19"> <install version="1.0"> <actions_group> <actions os="linux" architecture="x86_64"> <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> </actions> <actions os="darwin" architecture="x86_64"> <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> </actions> <actions> <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action> <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> <action type="shell_command">make</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>bcftools/bcftools</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>bcftools/vcfutils.pl</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>libbam.a</source> <destination>$INSTALL_DIR/lib</destination> </action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR/include/bam</destination_directory> </action> </actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> </action> </actions_group> </install> <readme> Program: samtools (Tools for alignments in the SAM format) Version: 0.1.19-44428cd Usage: samtools <command> [options] Command: view SAM<->BAM conversion sort sort alignment file mpileup multi-way pileup depth compute the depth faidx index/extract FASTA tview text alignment viewer index index alignment idxstats BAM index stats (r595 or later) fixmate fix mate information flagstat simple stats calmd recalculate MD/NM tags and '=' bases merge merge sorted alignments rmdup remove PCR duplicates reheader replace BAM header cat concatenate BAMs bedcov read depth per BED region targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes bamshuf shuffle and group alignments by name </readme> </package> <package name="VarScan" version="2.3.6"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> <action type="move_file"> <source>VarScan.v2.3.6.jar</source> <destination>$INSTALL_DIR/jars</destination> </action> <action type="set_environment"> <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> </action> </actions> </install> <readme> Downloads VarScan2. </readme> </package> <package name="VarScan" version="2.3.6"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> <action type="move_file"> <source>VarScan.v2.3.6.jar</source> <destination>$INSTALL_DIR/jars</destination> </action> <action type="set_environment"> <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable> </action> </actions> </install> <readme> Downloads VarScan2. </readme> </package> </tool_dependency>