Mercurial > repos > jason-ellul > calculatezprimefactor
diff tool_dependencies.xml @ 4:796653c6376b draft
Uploaded
| author | jason-ellul |
|---|---|
| date | Wed, 01 Jun 2016 02:36:11 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 01 02:36:11 2016 -0400 @@ -0,0 +1,135 @@ +<?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> +