Mercurial > repos > jason-ellul > calculatezprimefactor

comparison tool_dependencies.xml @ 4:796653c6376b draft

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author jason-ellul
date Wed, 01 Jun 2016 02:36:11 -0400
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3:8c9b1fa6c456 4:796653c6376b
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <!-- Optimized samtools (for threaded mpileup)
4 <package name="samtools-parallel-mpileup" version="0.1.19">
5 <install version="1.0">
6 <actions>
7 <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup &amp;&amp; cd samtools-parallel-mpileup &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-parallel-mpileup</action>
8 <action type="move_file">
9 <source>samtools-parallel-mpileup</source>
10 <destination>$INSTALL_DIR/bin</destination>
11 </action>
12 <action type="set_environment">
13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
14 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
15 </action>
16 </actions>
17 </install>
18 <readme>
19 Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
20 </readme>
21 </package>
22 -->
23 <package name="samtools" version="0.1.19">
24 <install version="1.0">
25 <actions_group>
26 <actions os="linux" architecture="x86_64">
27 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action>
28 <action type="move_directory_files">
29 <source_directory>.</source_directory>
30 <destination_directory>$INSTALL_DIR</destination_directory>
31 </action>
32 </actions>
33 <actions os="darwin" architecture="x86_64">
34 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action>
35 <action type="move_directory_files">
36 <source_directory>.</source_directory>
37 <destination_directory>$INSTALL_DIR</destination_directory>
38 </action>
39 </actions>
40 <actions>
41 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action>
42 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
43 <action type="shell_command">make</action>
44 <action type="move_file">
45 <source>samtools</source>
46 <destination>$INSTALL_DIR/bin</destination>
47 </action>
48 <action type="move_file">
49 <source>bcftools/bcftools</source>
50 <destination>$INSTALL_DIR/bin</destination>
51 </action>
52 <action type="move_file">
53 <source>bcftools/vcfutils.pl</source>
54 <destination>$INSTALL_DIR/bin</destination>
55 </action>
56 <action type="move_file">
57 <source>libbam.a</source>
58 <destination>$INSTALL_DIR/lib</destination>
59 </action>
60 <action type="move_directory_files">
61 <source_directory>.</source_directory>
62 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
63 </action>
64 </actions>
65 <action type="set_environment">
66 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
67 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
68 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
69 </action>
70 </actions_group>
71 </install>
72 <readme>
73 Program: samtools (Tools for alignments in the SAM format)
74 Version: 0.1.19-44428cd
75
76 Usage: samtools &lt;command&gt; [options]
77
78 Command: view SAM&lt;-&gt;BAM conversion
79 sort sort alignment file
80 mpileup multi-way pileup
81 depth compute the depth
82 faidx index/extract FASTA
83 tview text alignment viewer
84 index index alignment
85 idxstats BAM index stats (r595 or later)
86 fixmate fix mate information
87 flagstat simple stats
88 calmd recalculate MD/NM tags and '=' bases
89 merge merge sorted alignments
90 rmdup remove PCR duplicates
91 reheader replace BAM header
92 cat concatenate BAMs
93 bedcov read depth per BED region
94 targetcut cut fosmid regions (for fosmid pool only)
95 phase phase heterozygotes
96 bamshuf shuffle and group alignments by name
97 </readme>
98 </package>
99 <package name="VarScan" version="2.3.6">
100 <install version="1.0">
101 <actions>
102 <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
103 <action type="move_file">
104 <source>VarScan.v2.3.6.jar</source>
105 <destination>$INSTALL_DIR/jars</destination>
106 </action>
107 <action type="set_environment">
108 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
109 </action>
110 </actions>
111 </install>
112 <readme>
113 Downloads VarScan2.
114 </readme>
115 </package>
116
117 <package name="VarScan" version="2.3.6">
118 <install version="1.0">
119 <actions>
120 <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
121 <action type="move_file">
122 <source>VarScan.v2.3.6.jar</source>
123 <destination>$INSTALL_DIR/jars</destination>
124 </action>
125 <action type="set_environment">
126 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
127 </action>
128 </actions>
129 </install>
130 <readme>
131 Downloads VarScan2.
132 </readme>
133 </package>
134 </tool_dependency>
135