Mercurial > repos > devteam > package_samtools_0_1_16
changeset 0:75367f13eb3c draft
Uploaded tool_dependencies.xml
| author | devteam |
|---|---|
| date | Tue, 05 Feb 2013 14:17:34 -0500 |
| parents | |
| children | 3cc494fb5a14 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 47 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 05 14:17:34 2013 -0500 @@ -0,0 +1,47 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.16"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.16/samtools-0.1.16.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>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This is the last version of SAMTools to include the 'pileup' command. + +Program: samtools (Tools for alignments in the SAM format) +Version: 0.1.16 (r963:234) + +Usage: samtools <command> [options] + +Command: view SAM<->BAM conversion + sort sort alignment file + pileup generate pileup output + 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 + glfview print GLFv3 file + 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