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comparison tool_dependencies.xml @ 0:75367f13eb3c draft

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Uploaded tool_dependencies.xml
author devteam
date Tue, 05 Feb 2013 14:17:34 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="0.1.16">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.16/samtools-0.1.16.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 This is the last version of SAMTools to include the 'pileup' command.
20
21 Program: samtools (Tools for alignments in the SAM format)
22 Version: 0.1.16 (r963:234)
23
24 Usage: samtools &lt;command&gt; [options]
25
26 Command: view SAM&lt;-&gt;BAM conversion
27 sort sort alignment file
28 pileup generate pileup output
29 mpileup multi-way pileup
30 depth compute the depth
31 faidx index/extract FASTA
32 tview text alignment viewer
33 index index alignment
34 idxstats BAM index stats (r595 or later)
35 fixmate fix mate information
36 glfview print GLFv3 file
37 flagstat simple stats
38 calmd recalculate MD/NM tags and '=' bases
39 merge merge sorted alignments
40 rmdup remove PCR duplicates
41 reheader replace BAM header
42 cat concatenate BAMs
43 targetcut cut fosmid regions (for fosmid pool only)
44 phase phase heterozygotes
45 </readme>
46 </package>
47 </tool_dependency>