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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="biopython" version="1.61">
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2
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4 <repository changeset_revision="b482933a6de5" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <set_environment version="1.0">
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7 <environment_variable action="set_to" name="GLIMMER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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8 </set_environment>
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9 <package name="glimmer" version="3.02b">
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_file">http://www.cbcb.umd.edu/software/glimmer/glimmer302b.tar.gz</action>
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13 <action type="shell_command">tar xfvz glimmer302b.tar.gz</action>
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14 <action type="shell_command">cd ./glimmer3.02/src && make</action>
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15
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16 <action type="move_directory_files">
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17 <source_directory>./glimmer3.02/bin</source_directory>
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18 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>To compile glimmer you need a C compiler (usually gcc).
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26 Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
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27 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
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28 http://www.cbcb.umd.edu/software/glimmer/</readme>
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29 </package>
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30 </tool_dependency>
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