Mercurial > repos > bjoern-gruening > augustus

comparison tool_dependencies.xml @ 5:a4fab0c1ae1a

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author bjoern-gruening
date Sun, 09 Jun 2013 07:54:25 -0400
parents 796814f16b12
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4:796814f16b12 5:a4fab0c1ae1a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="augustus" version="2.6.1"> 3 <set_environment version="1.0">
4 <environment_variable name="AUGUSTUS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
5 </set_environment>
6 <package name="augustus" version="2.7">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <actions>
6 <!-- the first command puts us in the dir for the package name: "augustus"--> 9 <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.7.tar.gz</action>
7 <action type="download_by_url">http://bioinf.uni-greifswald.de/augustus/binaries/augustus.2.6.1.tar.gz</action>
8 <action type="shell_command">make</action> 10 <action type="shell_command">make</action>
9 <action type="move_directory_files"> 11 <action type="move_directory_files">
10 <source_directory>bin</source_directory> 12 <source_directory>bin</source_directory>
11 <destination_directory>$INSTALL_DIR/bin</destination_directory> 13 <destination_directory>$INSTALL_DIR/bin</destination_directory>
12 </action> 14 </action>
18 <source_directory>config</source_directory> 20 <source_directory>config</source_directory>
19 <destination_directory>$INSTALL_DIR/config</destination_directory> 21 <destination_directory>$INSTALL_DIR/config</destination_directory>
20 </action> 22 </action>
21 <action type="set_environment"> 23 <action type="set_environment">
22 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> 24 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
23 </action>
24 <action type="set_environment">
25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 25 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
26 </action>
27 <action type="set_environment">
28 <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable> 26 <environment_variable name="AUGUSTUS_CONFIG_PATH" action="set_to">$INSTALL_DIR/config</environment_variable>
29 </action> 27 </action>
30 </actions> 28 </actions>
31 </install> 29 </install>
32 <readme>http://augustus.gobics.de/binaries/README.TXT</readme> 30 <readme>AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
31 It can be used as an ab initio program, which means it bases its prediction purely on the
32 sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
33 such as EST, MS/MS, protein alignments and synthenic genomic alignments.
34 http://augustus.gobics.de/binaries/README.TXT</readme>
33 </package> 35 </package>
34 </tool_dependency> 36 </tool_dependency>