Mercurial > repos > shirish > samtools
changeset 1:4a8cd798d083 draft
Deleted selected files
| author | shirish |
|---|---|
| date | Tue, 03 Jun 2014 09:50:04 -0400 |
| parents | 9b2a3a7b73bd |
| children | fd17ccc9993b |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 0 insertions(+), 83 deletions(-) [+] |
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--- a/tool_dependencies.xml Tue Jun 03 08:05:16 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions_group> - <actions os="linux" architecture="i386"> - <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions os="linux" architecture="x86_64"> - <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions os="darwin" architecture="i386"> - <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions os="darwin" architecture="x86_64"> - <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <actions> - <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.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>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>libbam.a</source> - <destination>$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: 0.1.18 (r982:295) - -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 - </readme> - </package> -</tool_dependency> \ No newline at end of file