Mercurial > repos > jason-ellul > calculatezprimefactor
diff tool_dependencies.xml @ 5:d7efb5d5352a draft default tip
Uploaded
| author | jason-ellul |
|---|---|
| date | Wed, 01 Jun 2016 02:40:16 -0400 |
| parents | 796653c6376b |
| children |
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--- a/tool_dependencies.xml Wed Jun 01 02:36:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,135 +0,0 @@ -<?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> -