Mercurial > repos > lionelguy > prokka

annotate tool_dependencies.xml @ 10:2720b1e27a9c draft

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Added dependency for infernal
author lionelguy
date Fri, 06 Sep 2013 05:38:49 -0400
parents 6acf850bca99
children f2cc11ac2006
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2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="hmmer" version="3.1b1">
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4 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="blast+" version="2.2.26+">
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7 <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="aragorn" version="1.2.36">
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10 <repository changeset_revision="d34f31cbc9dd" name="trna_prediction" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="prodigal" version="2.60">
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13 <repository changeset_revision="304c1a67bb7b" name="prodigal" owner="edward-kirton" toolshed="http://toolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="package_barrnap_0_1" version="0.1">
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16 <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" />
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17 </package>
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18 <package name="infernal" version="1.1rc4">
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19 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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20 </package> --&gt;
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21 <package name="prokka" version="1.7">
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22 <install version="1.0">
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23 <actions>
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24 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
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25 <!-- Copying the whole bin, binaries, doc and db folders -->
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26 <action type="make_directory">$INSTALL_DIR/bin</action>
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27 <action type="make_directory">$INSTALL_DIR/binaries</action>
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28 <action type="make_directory">$INSTALL_DIR/db</action>
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29 <action type="make_directory">$INSTALL_DIR/doc</action>
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30 <action type="move_directory_files">
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31 <source_directory>bin</source_directory>
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32 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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33 </action>
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34 <action type="move_directory_files">
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35 <source_directory>binaries</source_directory>
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36 <destination_directory>$INSTALL_DIR/binaries</destination_directory>
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37 </action>
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38 <action type="move_directory_files">
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39 <source_directory>db</source_directory>
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40 <destination_directory>$INSTALL_DIR/db</destination_directory>
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41 </action>
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42 <action type="move_directory_files">
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43 <source_directory>doc</source_directory>
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44 <destination_directory>$INSTALL_DIR/doc</destination_directory>
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45 </action>
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46 <action type="set_environment">
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47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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48 </action>
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49 </actions>
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50 </install>
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51 <readme>
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52 This installs prokka 1.7
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53 Note: this is about a 2.0 GB download due to included custom databases.</readme>
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54 </package>
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55 </tool_dependency>