Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
view tool_dependencies.xml @ 42:bf9c5a61b200
overwrite readonly files
author | yhoogstrate <y.hoogstrate@erasmusmc.nl> |
---|---|
date | Wed, 05 Mar 2014 13:34:36 +0100 |
parents | |
children | ef13be78c5fc |
line wrap: on
line source
<?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> <!-- Classical samtools (doesn't support threaded mpileup) --> <package name="samtools" version="0.1.19"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/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="shell_command">chmod ugo+rx misc/*.p?</action> <action type="shell_command">mkdir misc/bin</action> <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</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>$INSTALL_DIR/bin</destination> </action> <action type="move_directory_files"> <source_directory>misc/bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> Program: samtools (Tools for alignments in the SAM format) Version: 0.1.19 Usage: samtools <command> [options] Command: view SAM<->BAM conversion sort sort alignment file mpileup multi-way pileup depth compute the depth faidx index/extract FASTA tview text alignment viewer index index alignment idxstats BAM index stats (r595 or later) fixmate fix mate information flagstat simple stats calmd recalculate MD/NM tags and '=' bases merge merge sorted alignments rmdup remove PCR duplicates reheader replace BAM header cat concatenate BAMs targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes This also installs bcftools and misc utility commands: bcftools vcfutils.pl ace2sam bamcheck blast2sam.pl bowtie2sam.pl export2sam.pl interpolate_sam.pl maq2sam-long maq2sam-short md5fa md5sum-lite novo2sam.pl psl2sam.pl sam2vcf.pl samtools.pl soap2sam.pl varfilter.py wgsim wgsim_eval.pl zoom2sam.pl </readme> </package> <package name="VarScan" version="2.3.6"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action> <action type="move_file"> <source>VarScan.v2.3.6.jar</source> <destination>$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>