Mercurial > repos > lionelguy > prokka

comparison tool_dependencies.xml @ 8:6acf850bca99 draft

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Replaced the repository_dependencies by tool_dependencies
author lionelguy
date Fri, 06 Sep 2013 02:42:23 -0400
parents 2bb7c28ea68f
children 2720b1e27a9c
comparison
equal deleted inserted replaced
7:39bc9c61c55b 8:6acf850bca99
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="prokka" version="1.7"> 3 <package name="hmmer" version="3.1b1">
4 <install version="1.0"> 4 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
5 <actions> 5 </package>
6 <package name="blast+" version="2.2.26+">
7 <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="aragorn" version="1.2.36">
10 <repository changeset_revision="d34f31cbc9dd" name="trna_prediction" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="prodigal" version="2.60">
13 <repository changeset_revision="304c1a67bb7b" name="prodigal" owner="edward-kirton" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="package_barrnap_0_1" version="0.1">
16 <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" />
17 </package>
18 <!--<package name="infernal" version="1.1rc4">
19 <repository name="package_infernal_1_1rc4" owner="iuc" />
20 </package> -->
21 <package name="prokka" version="1.7">
22 <install version="1.0">
23 <actions>
6 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> 24 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
7 <!-- Copying the whole bin, binaries, doc and db folders --> 25 <!-- Copying the whole bin, binaries, doc and db folders -->
8 <action type="make_directory">$INSTALL_DIR/bin</action> 26 <action type="make_directory">$INSTALL_DIR/bin</action>
9 <action type="make_directory">$INSTALL_DIR/binaries</action> 27 <action type="make_directory">$INSTALL_DIR/binaries</action>
10 <action type="make_directory">$INSTALL_DIR/db</action> 28 <action type="make_directory">$INSTALL_DIR/db</action>
11 <action type="make_directory">$INSTALL_DIR/doc</action> 29 <action type="make_directory">$INSTALL_DIR/doc</action>
12 <action type="move_directory_files">
13 <source_directory>bin</source_directory>
14 <destination_directory>$INSTALL_DIR/bin</destination_directory>
15 </action>
16 <action type="move_directory_files"> 30 <action type="move_directory_files">
17 <source_directory>binaries</source_directory> 31 <source_directory>bin</source_directory>
18 <destination_directory>$INSTALL_DIR/binaries</destination_directory> 32 <destination_directory>$INSTALL_DIR/bin</destination_directory>
19 </action> 33 </action>
20 <action type="move_directory_files"> 34 <action type="move_directory_files">
21 <source_directory>db</source_directory> 35 <source_directory>binaries</source_directory>
22 <destination_directory>$INSTALL_DIR/db</destination_directory> 36 <destination_directory>$INSTALL_DIR/binaries</destination_directory>
23 </action> 37 </action>
24 <action type="move_directory_files"> 38 <action type="move_directory_files">
25 <source_directory>doc</source_directory> 39 <source_directory>db</source_directory>
26 <destination_directory>$INSTALL_DIR/doc</destination_directory> 40 <destination_directory>$INSTALL_DIR/db</destination_directory>
27 </action> 41 </action>
42 <action type="move_directory_files">
43 <source_directory>doc</source_directory>
44 <destination_directory>$INSTALL_DIR/doc</destination_directory>
45 </action>
28 <action type="set_environment"> 46 <action type="set_environment">
29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
30 </action> 48 </action>
31 </actions> 49 </actions>
32 </install> 50 </install>
33
34 <readme> 51 <readme>
35 This installs prokka 1.7 52 This installs prokka 1.7
36 Note: this is about a 2.0 GB download due to included custom databases.</readme> 53 Note: this is about a 2.0 GB download due to included custom databases.</readme>
37 </package> 54 </package>
38 </tool_dependency> 55 </tool_dependency>