Mercurial > repos > lionelguy > prokka

annotate tool_dependencies.xml @ 11:f2cc11ac2006 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author lionelguy
date Fri, 06 Sep 2013 05:39:47 -0400
parents 2720b1e27a9c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
1 <?xml version="1.0"?>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
2 <tool_dependency>
8
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
3 <package name="hmmer" version="3.1b1">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
4 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
5 </package>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
6 <package name="blast+" version="2.2.26+">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
7 <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
8 </package>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
9 <package name="aragorn" version="1.2.36">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
10 <repository changeset_revision="d34f31cbc9dd" name="trna_prediction" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" />
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
11 </package>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
12 <package name="prodigal" version="2.60">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
13 <repository changeset_revision="304c1a67bb7b" name="prodigal" owner="edward-kirton" toolshed="http://toolshed.g2.bx.psu.edu" />
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
14 </package>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
15 <package name="package_barrnap_0_1" version="0.1">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
16 <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" />
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
17 </package>
10
2720b1e27a9c Added dependency for infernal
lionelguy
parents: 8
diff changeset
18 <package name="infernal" version="1.1rc4">
2720b1e27a9c Added dependency for infernal
lionelguy
parents: 8
diff changeset
19 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
11
f2cc11ac2006 Uploaded
lionelguy
parents: 10
diff changeset
20 </package>
8
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
21 <package name="prokka" version="1.7">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
22 <install version="1.0">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
23 <actions>
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
24 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
25 <!-- Copying the whole bin, binaries, doc and db folders -->
8
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
26 <action type="make_directory">$INSTALL_DIR/bin</action>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
27 <action type="make_directory">$INSTALL_DIR/binaries</action>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
28 <action type="make_directory">$INSTALL_DIR/db</action>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
29 <action type="make_directory">$INSTALL_DIR/doc</action>
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
30 <action type="move_directory_files">
8
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
31 <source_directory>bin</source_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
32 <destination_directory>$INSTALL_DIR/bin</destination_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
33 </action>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
34 <action type="move_directory_files">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
35 <source_directory>binaries</source_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
36 <destination_directory>$INSTALL_DIR/binaries</destination_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
37 </action>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
38 <action type="move_directory_files">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
39 <source_directory>db</source_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
40 <destination_directory>$INSTALL_DIR/db</destination_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
41 </action>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
42 <action type="move_directory_files">
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
43 <source_directory>doc</source_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
44 <destination_directory>$INSTALL_DIR/doc</destination_directory>
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
45 </action>
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
46 <action type="set_environment">
8
6acf850bca99 Replaced the repository_dependencies by tool_dependencies
lionelguy
parents: 1
diff changeset
47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
1
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
48 </action>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
49 </actions>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
50 </install>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
51 <readme>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
52 This installs prokka 1.7
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
53 Note: this is about a 2.0 GB download due to included custom databases.</readme>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
54 </package>
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
lionelguy
parents:
diff changeset
55 </tool_dependency>