Mercurial > repos > jjohnson > samtools_0_1_18
comparison tool_dependencies.xml @ 0:e9da9a990458 draft default tip
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| author | jjohnson |
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| date | Tue, 19 Feb 2013 21:53:32 -0500 |
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| -1:000000000000 | 0:e9da9a990458 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="samtools" version="0.1.18"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> | |
| 7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | |
| 8 <action type="shell_command">make</action> | |
| 9 <action type="move_file"> | |
| 10 <source>samtools</source> | |
| 11 <destination>$INSTALL_DIR/bin</destination> | |
| 12 </action> | |
| 13 <action type="set_environment"> | |
| 14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 15 </action> | |
| 16 </actions> | |
| 17 </install> | |
| 18 <readme> | |
| 19 Program: samtools (Tools for alignments in the SAM format) | |
| 20 Version: 0.1.18 (r982:295) | |
| 21 | |
| 22 Usage: samtools <command> [options] | |
| 23 | |
| 24 Command: view SAM<->BAM conversion | |
| 25 sort sort alignment file | |
| 26 mpileup multi-way pileup | |
| 27 depth compute the depth | |
| 28 faidx index/extract FASTA | |
| 29 tview text alignment viewer | |
| 30 index index alignment | |
| 31 idxstats BAM index stats (r595 or later) | |
| 32 fixmate fix mate information | |
| 33 flagstat simple stats | |
| 34 calmd recalculate MD/NM tags and '=' bases | |
| 35 merge merge sorted alignments | |
| 36 rmdup remove PCR duplicates | |
| 37 reheader replace BAM header | |
| 38 cat concatenate BAMs | |
| 39 targetcut cut fosmid regions (for fosmid pool only) | |
| 40 phase phase heterozygotes | |
| 41 </readme> | |
| 42 </package> | |
| 43 </tool_dependency> |