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comparison tool_dependencies.xml @ 7:1ea6445491d4 draft

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Update to deFuse version 0.6.0
author Jim Johnson <jj@umn.edu>
date Mon, 07 Jan 2013 14:52:26 -0600
parents 3bd1087db05e
children b22f8634ff84
comparison
equal deleted inserted replaced
6:6e30713cefb0 7:1ea6445491d4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="defuse" version="0.5.0"> 3 <package name="defuse" version="0.6.0">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.5/defuse-0.5.0.tar.gz</action> 6 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
7 <action type="shell_command">cd tools &amp;&amp; make</action> 7 <action type="shell_command">cd tools &amp;&amp; make</action>
8 <action type="move_directory_files"> 8 <action type="move_directory_files">
9 <source_directory>.</source_directory> 9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory> 10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action> 11 </action>
13 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable> 13 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
14 </action> 14 </action>
15 </actions> 15 </actions>
16 </install> 16 </install>
17 <readme> 17 <readme>
18 deFuse code
19 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
18 </readme> 20 </readme>
19 </package> 21 </package>
22
23 <package name="samtools" version="0.1.18">
24 <install version="1.0">
25 <actions>
26 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
27 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
28 <action type="shell_command">make</action>
29 <action type="move_file">
30 <source>samtools</source>
31 <destination>$INSTALL_DIR/bin</destination>
32 </action>
33 <action type="move_file">
34 <source>misc/maq2sam-long</source>
35 <destination>$INSTALL_DIR/bin</destination>
36 </action>
37 <action type="set_environment">
38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
39 </action>
40 </actions>
41 </install>
42 <readme>
43 Compiling SAMtools requires the ncurses and zlib development libraries.
44 </readme>
45 </package>
46
20 47
21 <package name="bowtie" version="0.12.7"> 48 <package name="bowtie" version="0.12.7">
22 <install version="1.0"> 49 <install version="1.0">
23 <actions> 50 <actions>
24 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action> 51 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
40 </action> 67 </action>
41 </actions> 68 </actions>
42 </install> 69 </install>
43 <readme> 70 <readme>
44 Compiling Bowtie requires libpthread to be present on your system. 71 Compiling Bowtie requires libpthread to be present on your system.
72 </readme>
73 </package>
74
75 <package name="gmap" version="2012-07-20">
76 <install version="1.0">
77 <actions>
78 <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action>
79 <action type="shell_command">./configure</action>
80 <action type="shell_command">make</action>
81 <action type="move_file">
82 <source>src/gmap</source>
83 <destination>$INSTALL_DIR/bin</destination>
84 </action>
85 <action type="move_file">
86 <source>src/gmapindex</source>
87 <destination>$INSTALL_DIR/bin</destination>
88 </action>
89 <action type="move_file">
90 <source>src/gsnap</source>
91 <destination>$INSTALL_DIR/bin</destination>
92 </action>
93 <action type="move_file">
94 <source>src/uniqscan</source>
95 <destination>$INSTALL_DIR/bin</destination>
96 </action>
97 <action type="move_file">
98 <source>src/iit_store</source>
99 <destination>$INSTALL_DIR/bin</destination>
100 </action>
101 <action type="move_file">
102 <source>src/iit_get</source>
103 <destination>$INSTALL_DIR/bin</destination>
104 </action>
105 <action type="move_file">
106 <source>src/atoiindex</source>
107 <destination>$INSTALL_DIR/bin</destination>
108 </action>
109 <action type="move_file">
110 <source>src/snpindex</source>
111 <destination>$INSTALL_DIR/bin</destination>
112 </action>
113 <action type="move_file">
114 <source>src/cmetindex</source>
115 <destination>$INSTALL_DIR/bin</destination>
116 </action>
117 <action type="move_file">
118 <source>src/get-genome</source>
119 <destination>$INSTALL_DIR/bin</destination>
120 </action>
121 <action type="move_directory_files">
122 <source_directory>util</source_directory>
123 <destination_directory>$INSTALL_DIR/bin</destination_directory>
124 </action>
125 <action type="set_environment">
126 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
127 </action>
128 </actions>
129 </install>
130 <readme>
45 </readme> 131 </readme>
46 </package> 132 </package>
47 133
48 <package name="blat" version="34x10"> 134 <package name="blat" version="34x10">
49 <install version="1.0"> 135 <install version="1.0">