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comparison tool_dependencies.xml @ 49:f008ab2cadc6 draft

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author big-tiandm
date Wed, 03 Dec 2014 02:03:27 -0500
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children 7b5a48b972e9
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48:28ad3b598670 49:f008ab2cadc6
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="fastx_toolkit" version="0.0.13">
4 <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="bowtie" version="0.12.7">
7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <set_environment version="1.0">
10 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
11 </set_environment>
12 <!--package name="R" version="3.0.1">
13 <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package!-->
15
16 <package name="ViennaRNA" version="2.1.8">
17 <install version="1.0">
18 <actions>
19 <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
20 <action type="shell_command">./configure --prefix=$INSTALL_DIR </action>
21 <action type="shell_command">make</action>
22 <action type="shell_command">make install</action>
23 <action type="set_environment">
24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
25 </action>
26 </actions>
27 </install>
28 </package>
29
30 <package name="SVG" version="2.59">
31 <install version="1.0">
32 <actions>
33 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
34 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
35 <action type="shell_command">
36 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
37 make &amp;&amp;
38 make install
39 </action>
40 <action type="set_environment">
41 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
42 </action>
43 </actions>
44 </install>
45 </package>
46
47
48 </tool_dependency>