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comparison tool_dependencies.xml @ 0:302d166cd10d draft default tip

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author hyungrolee
date Tue, 02 Feb 2016 01:51:30 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="tandem_repeats_finder" version="4.0">
4 <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="mgescan" version="3">
7 <install version="1.0">
8 <actions_group>
9 <actions architecture="x86_64" os="linux">
10 <action type="download_by_url">
11 https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
12 </action>
13 <action type="move_directory_files">
14 <source_directory>.</source_directory>
15 <destination_directory>$INSTALL_DIR</destination_directory>
16 </action>
17 </actions>
18 <actions>
19 <action type="download_by_url">
20 https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
21 </action>
22 <action type="set_environment_for_install">
23 <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" toolshed="https://toolshed.g2.bx.psu.edu">
24 <package name="trf" version="4.0" />
25 </repository>
26 </action>
27 <action type="shell_command">cd mgescan-1.0</action>
28 <action type="shell_command">python setup.py install</action>
29 <action type="move_file">
30 <source>mgescan</source>
31 <destination>$INSTALL_DIR/bin</destination>
32 </action>
33 </actions>
34 <action type="set_environment">
35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
36 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
37 </action>
38 </actions_group>
39 </install>
40 <readme>
41 Program: mgescan (Tools for identifying LTR &amp; nonLTR)
42 Version: 3.0
43
44 Usage:
45 mgescan both &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
46 mgescan ltr &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
47 mgescan nonltr &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
48 mgescan (-h | --help)
49 mgescan --version
50
51 </readme>
52 </package>
53 </tool_dependency>