Mercurial > repos > iuc > package_samtools_0_1_18

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author iuc
date Mon, 06 Apr 2015 17:46:11 -0400
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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_group>
6 <actions os="linux" architecture="i386">
7 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <actions os="linux" architecture="x86_64">
14 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 </actions>
20 <actions os="darwin" architecture="i386">
21 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
22 <action type="move_directory_files">
23 <source_directory>.</source_directory>
24 <destination_directory>$INSTALL_DIR</destination_directory>
25 </action>
26 </actions>
27 <actions os="darwin" architecture="x86_64">
28 <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
29 <action type="move_directory_files">
30 <source_directory>.</source_directory>
31 <destination_directory>$INSTALL_DIR</destination_directory>
32 </action>
33 </actions>
34 <actions>
35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.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 <action type="move_directory_files">
47 <source_directory>.</source_directory>
48 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
49 </action>
50 </actions>
51 <action type="set_environment">
52 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
53 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
54 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
55 </action>
56 </actions_group>
57 </install>
58 <readme>
59 Program: samtools (Tools for alignments in the SAM format)
60 Version: 0.1.18 (r982:295)
61
62 Usage: samtools &lt;command&gt; [options]
63
64 Command: view SAM&lt;-&gt;BAM conversion
65 sort sort alignment file
66 mpileup multi-way pileup
67 depth compute the depth
68 faidx index/extract FASTA
69 tview text alignment viewer
70 index index alignment
71 idxstats BAM index stats (r595 or later)
72 fixmate fix mate information
73 flagstat simple stats
74 calmd recalculate MD/NM tags and '=' bases
75 merge merge sorted alignments
76 rmdup remove PCR duplicates
77 reheader replace BAM header
78 cat concatenate BAMs
79 targetcut cut fosmid regions (for fosmid pool only)
80 phase phase heterozygotes
81 </readme>
82 </package>
83 </tool_dependency>