|
0
|
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> |
