comparison tool_dependencies.xml @ 0:cb87eae7fc3e

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author iuc
date Mon, 19 Aug 2013 17:19:38 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="0.1.19">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.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: 0.1.19
21
22 Usage: samtools &lt;command&gt; [options]
23
24 Command: view SAM&lt;-&gt;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>