annotate tool_dependencies.xml @ 9:9f30de0ff090 draft

Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
author Jim Johnson <jj@umn.edu>
date Mon, 14 Jan 2013 11:26:17 -0600
parents 1ea6445491d4
children b22f8634ff84
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 <?xml version="1.0"?>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <tool_dependency>
7
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
3 <package name="defuse" version="0.6.0">
4
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 <install version="1.0">
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 <actions>
7
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
6 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action>
4
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 <action type="shell_command">cd tools &amp;&amp; make</action>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 <action type="move_directory_files">
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 <source_directory>.</source_directory>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 <destination_directory>$INSTALL_DIR</destination_directory>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 </action>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 <action type="set_environment">
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 </action>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 </actions>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 </install>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 <readme>
7
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
18 deFuse code
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
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/:$CPLUS_INCLUDE_PATH`)
4
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 </readme>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 </package>
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22
7
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
23 <package name="samtools" version="0.1.18">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
24 <install version="1.0">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
25 <actions>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
26 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
27 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
28 <action type="shell_command">make</action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
29 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
30 <source>samtools</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
31 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
32 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
33 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
34 <source>misc/maq2sam-long</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
35 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
36 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
37 <action type="set_environment">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
39 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
40 </actions>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
41 </install>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
42 <readme>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
43 Compiling SAMtools requires the ncurses and zlib development libraries.
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
44 </readme>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
45 </package>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
46
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
47
5
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
48 <package name="bowtie" version="0.12.7">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
49 <install version="1.0">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
50 <actions>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
51 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
52 <action type="shell_command">make</action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
53 <action type="move_file">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
54 <source>bowtie</source>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
55 <destination>$INSTALL_DIR/bin</destination>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
56 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
57 <action type="move_file">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
58 <source>bowtie-build</source>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
59 <destination>$INSTALL_DIR/bin</destination>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
60 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
61 <action type="move_file">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
62 <source>bowtie-inspect</source>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
63 <destination>$INSTALL_DIR/bin</destination>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
64 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
65 <action type="set_environment">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
66 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
67 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
68 </actions>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
69 </install>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
70 <readme>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
71 Compiling Bowtie requires libpthread to be present on your system.
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
72 </readme>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
73 </package>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
74
7
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
75 <package name="gmap" version="2012-07-20">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
76 <install version="1.0">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
77 <actions>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
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>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
79 <action type="shell_command">./configure</action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
80 <action type="shell_command">make</action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
81 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
82 <source>src/gmap</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
83 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
84 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
85 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
86 <source>src/gmapindex</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
87 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
88 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
89 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
90 <source>src/gsnap</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
91 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
92 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
93 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
94 <source>src/uniqscan</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
95 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
96 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
97 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
98 <source>src/iit_store</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
99 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
100 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
101 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
102 <source>src/iit_get</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
103 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
104 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
105 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
106 <source>src/atoiindex</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
107 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
108 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
109 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
110 <source>src/snpindex</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
111 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
112 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
113 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
114 <source>src/cmetindex</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
115 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
116 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
117 <action type="move_file">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
118 <source>src/get-genome</source>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
119 <destination>$INSTALL_DIR/bin</destination>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
120 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
121 <action type="move_directory_files">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
122 <source_directory>util</source_directory>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
123 <destination_directory>$INSTALL_DIR/bin</destination_directory>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
124 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
125 <action type="set_environment">
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
126 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
127 </action>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
128 </actions>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
129 </install>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
130 <readme>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
131 </readme>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
132 </package>
1ea6445491d4 Update to deFuse version 0.6.0
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
133
5
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
134 <package name="blat" version="34x10">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
135 <install version="1.0">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
136 <actions>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
137 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
138 <action type="shell_command">chmod 755 blat</action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
139 <action type="move_file">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
140 <source>blat</source>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
141 <destination>$INSTALL_DIR/bin</destination>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
142 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
143 <action type="set_environment">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
144 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
145 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
146 </actions>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
147 </install>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
148 <readme>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
149 This only handles blat for a non-commercial linux system.
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
150
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
151 Please note that the Blat source and executables are freely available for
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
152 academic, nonprofit and personal use. Commercial licensing information is
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
153 available on the Kent Informatics website (http://www.kentinformatics.com/).
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
154 </readme>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
155 </package>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
156
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
157 <package name="fatotwobit" version="34x10">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
158 <install version="1.0">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
159 <actions>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
160 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
161 <action type="shell_command">chmod 755 faToTwoBit</action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
162 <action type="move_file">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
163 <source>faToTwoBit</source>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
164 <destination>$INSTALL_DIR/bin</destination>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
165 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
166 <action type="set_environment">
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
167 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
168 </action>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
169 </actions>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
170 </install>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
171 <readme>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
172 This only handles faToTwoBit for a non-commercial linux system.
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
173
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
174 Please note that the source and executables are freely available for
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
175 academic, nonprofit and personal use. Commercial licensing information is
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
176 available on the Kent Informatics website (http://www.kentinformatics.com/).
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
177 </readme>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
178 </package>
3bd1087db05e Add dependecies for bowtie, blat, and faToTwoBit
Jim Johnson <jj@umn.edu>
parents: 4
diff changeset
179
4
679a5c7b1294 deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
diff changeset
180 </tool_dependency>