# HG changeset patch # User shirish # Date 1401803423 14400 # Node ID fd17ccc9993b1072208f0f86d8e85d1e52a71f18 # Parent 4a8cd798d083be6a4d73ae667a1fdc78e89225ac Uploaded diff -r 4a8cd798d083 -r fd17ccc9993b tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 03 09:50:23 2014 -0400 @@ -0,0 +1,83 @@ + + + + + + + http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz + + . + $INSTALL_DIR + + + + http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz + + . + $INSTALL_DIR + + + + http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz + + . + $INSTALL_DIR + + + + http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz + + . + $INSTALL_DIR + + + + http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2 + sed -i.bak 's/-lcurses/-lncurses/' Makefile + make + + samtools + $INSTALL_DIR/bin + + + libbam.a + $INSTALL_DIR/lib + + + . + $INSTALL_DIR/include/bam + + + + $INSTALL_DIR/bin + $INSTALL_DIR/lib + $INSTALL_DIR + + + + +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 + + + \ No newline at end of file