Mercurial > repos > jjohnson > snpeff_with_dep

comparison tool_dependencies.xml @ 12:57c46f7fe70b

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tool_dependencies.xml changes
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 14:42:09 -0500
parents e9e4ff80e72b
children d57983929080
comparison
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11:e9e4ff80e72b 12:57c46f7fe70b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <set_environment version="1.0"> 3 <set_environment version="1.0">
4 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable> 4 <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/snpEff</environment_variable>
5 </set_environment> 5 </set_environment>
6 <package name="snpEff" version="3.0"> 6 <package name="snpEff" version="3.0">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip</action> 9 <action type="shell_command">wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff</action>
10 <action type="move_file"> 10 <action type="move_directory_files">
11 <source>snpEff_v3_0_core.zip</source> 11 <source_directory>.</source_directory>
12 <destination>$INSTALL_DIR</destination> 12 <destination_directory>$INSTALL_DIR</destination_directory>
13 </action> 13 </action>
14 <action type="shell_command">unzip snpEff_v3_0_core.zip</action> 14
15 <action type="shell_command">ln -s snpEff_3_0 bin</action>
16 <action type="set_environment"> 15 <action type="set_environment">
17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable>
18 </action> 17 </action>
19 </actions> 18 </actions>
20 </install> 19 </install>
21 <readme> 20 <readme>
22 </readme> 21 </readme>