Mercurial > repos > bjoern-gruening > augustus
comparison tool_dependencies.xml @ 5:a4fab0c1ae1a
Uploaded
| author | bjoern-gruening |
|---|---|
| date | Sun, 09 Jun 2013 07:54:25 -0400 |
| parents | 796814f16b12 |
| children |
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| 4:796814f16b12 | 5:a4fab0c1ae1a |
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| 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> |