Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
diff 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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Mar 05 13:34:36 2014 +0100 @@ -0,0 +1,120 @@ +<?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> \ No newline at end of file