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comparison tool_dependencies.xml @ 4:a0ea0f7ae029 draft

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Fixed the version number in tool_deps
author lionelguy
date Thu, 12 Sep 2013 07:48:30 -0400
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3:d82f18c76309 4:a0ea0f7ae029
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="spades" version="2.5.1">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action>
7 <!-- Copying the whole bin folder -->
8 <action type="make_directory">$INSTALL_DIR/bin</action>
9 <action type="make_directory">$INSTALL_DIR/share</action>
10 <action type="move_directory_files">
11 <source_directory>bin</source_directory>
12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
13 </action>
14 <action type="move_directory_files">
15 <source_directory>share</source_directory>
16 <destination_directory>$INSTALL_DIR/share</destination_directory>
17 </action>
18 <!-- This is required to have spades accept .dat files -->
19 <!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
20 <!-- <action type="set_environment"> -->
21 <!-- <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
22 <!-- </action> -->
23 </actions>
24 </install>
25 <readme>
26 This installs SPAdes 2.5.1.
27
28 See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html
29 See also here http://bioinf.spbau.ru/en/spades
30 </readme>
31 </package>
32 </tool_dependency>
33