Mercurial > repos > fcaramia > methylation_analysis_bismark

comparison tool_dependencies.xml @ 14:cdb7231da7f2 draft

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author fcaramia
date Mon, 17 Jun 2013 21:44:43 -0400
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children d2ba233899b0
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13:4eeda563e6c1 14:cdb7231da7f2
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <set_environment version="1.0">
4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
5 </set_environment>
6 <package name="bowtie2" version="2.0.0-beta7">
7 <install version="1.0">
8 <actions>
9 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
10 <action type="shell_command">make</action>
11 <action type="move_file">
12 <source>bowtie2</source>
13 <destination>$INSTALL_DIR/bin</destination>
14 </action>
15 <action type="move_file">
16 <source>bowtie2-align</source>
17 <destination>$INSTALL_DIR/bin</destination>
18 </action>
19 <action type="move_file">
20 <source>bowtie2-build</source>
21 <destination>$INSTALL_DIR/bin</destination>
22 </action>
23 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
24 <action type="set_environment">
25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
26 </action>
27 </actions>
28 </install>
29 <readme>
30 Compiling bowtie2 requires zlib and libpthread to be present on your system.
31 </readme>
32 </package>
33 <package name="bowtie" version="0.12.8">
34 <install version="1.0">
35 <actions>
36 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
37 <action type="shell_command">make</action>
38 <action type="move_file">
39 <source>bowtie</source>
40 <destination>$INSTALL_DIR/bin</destination>
41 </action>
42 <action type="move_file">
43 <source>bowtie-inspect</source>
44 <destination>$INSTALL_DIR/bin</destination>
45 </action>
46 <action type="move_file">
47 <source>bowtie-build</source>
48 <destination>$INSTALL_DIR/bin</destination>
49 </action>
50 <action type="set_environment">
51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
52 </action>
53 </actions>
54 </install>
55 <readme>
56 </readme>
57 </package>
58 </tool_dependency>