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author iuc
date Mon, 06 Apr 2015 17:46:06 -0400
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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_group>
6 <actions os="linux" architecture="i386">
7 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <actions os="linux" architecture="x86_64">
14 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 </actions>
20 <actions os="darwin" architecture="i386">
21 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
22 <action type="move_directory_files">
23 <source_directory>.</source_directory>
24 <destination_directory>$INSTALL_DIR</destination_directory>
25 </action>
26 </actions>
27 <actions os="darwin" architecture="x86_64">
28 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
29 <action type="move_directory_files">
30 <source_directory>.</source_directory>
31 <destination_directory>$INSTALL_DIR</destination_directory>
32 </action>
33 </actions>
34 <actions>
35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
36 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
37 <action type="shell_command">make</action>
38 <action type="move_file">
39 <source>samtools</source>
40 <destination>$INSTALL_DIR/bin</destination>
41 </action>
42 <action type="move_file">
43 <source>libbam.a</source>
44 <destination>$INSTALL_DIR/lib</destination>
45 </action>
46 </actions>
47 <action type="set_environment">
48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
49 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
50 </action>
51 </actions_group>
52 </install>
53 <readme>
54 This is the last version of SAMTools to include the 'pileup' command.
55
56 Program: samtools (Tools for alignments in the SAM format)
57 Version: 0.1.16 (r963:234)
58
59 Usage: samtools &lt;command&gt; [options]
60
61 Command: view SAM&lt;-&gt;BAM conversion
62 sort sort alignment file
63 pileup generate pileup output
64 mpileup multi-way pileup
65 depth compute the depth
66 faidx index/extract FASTA
67 tview text alignment viewer
68 index index alignment
69 idxstats BAM index stats (r595 or later)
70 fixmate fix mate information
71 glfview print GLFv3 file
72 flagstat simple stats
73 calmd recalculate MD/NM tags and '=' bases
74 merge merge sorted alignments
75 rmdup remove PCR duplicates
76 reheader replace BAM header
77 cat concatenate BAMs
78 targetcut cut fosmid regions (for fosmid pool only)
79 phase phase heterozygotes
80 </readme>
81 </package>
82 </tool_dependency>