Mercurial > repos > bjoern-gruening > augustus

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