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comparison tool_dependencies.xml @ 0:87fe81de0931 draft default tip

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author bigrna
date Sun, 04 Jan 2015 02:47:25 -0500
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-1:000000000000 0:87fe81de0931
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 <package name="R" version="3.0.1">
30 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
31
32 <install version="1.0">
33 <actions>
34 <action type="set_environment_for_install">
35 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
36 <package name="R" version="3.0.1" />
37 </repository>
38 </action>
39 <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
40 <action type="shell_command">echo "export PATH=$PATH" &gt; $INSTALL_DIR/env.sh </action>
41 <action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>
42
43 </actions>
44 </install>
45 </package>
46
47 <package name="threads" version="1.96">
48 <install version="1.0">
49 <actions>
50 <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
51 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
52 <action type="shell_command">
53 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
54 make &amp;&amp;
55 make install
56 </action>
57 <action type="set_environment">
58 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
59 </action>
60 </actions>
61 </install>
62 </package>
63
64
65 <package name="Parallel-ForkManager" version="1.06">
66 <install version="1.0">
67 <actions>
68 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
69 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
70 <action type="shell_command">
71 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
72 make &amp;&amp;
73 make install
74 </action>
75 <action type="set_environment">
76 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
77 </action>
78 </actions>
79 </install>
80 </package>
81
82 <package name="Boost-Graph" version="1.4_001">
83 <install version="1.0">
84 <actions>
85 <action type="download_by_url">http://www.cpan.org/authors/id/D/DU/DUFFEE/Boost-Graph-1.4_001.tar.gz</action>
86 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
87 <action type="shell_command">
88 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
89 ls &amp;&amp;
90 make &amp;&amp;
91 make install
92 </action>
93 <action type="set_environment">
94 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
95 </action>
96 </actions>
97 </install>
98 </package>
99
100 <package name="SVG" version="2.59">
101 <install version="1.0">
102 <actions>
103 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
104 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
105 <action type="shell_command">
106 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
107 make &amp;&amp;
108 make install
109 </action>
110 <action type="set_environment">
111 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
112 </action>
113 </actions>
114 </install>
115 </package>
116
117 <!--package name="parent" version="0.228">
118 <install version="1.0">
119 <actions>
120 <action type="download_by_url">http://www.cpan.org/authors/id/C/CO/CORION/parent-0.228.tar.gz</action>
121 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
122 <action type="shell_command">
123 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
124 make &amp;&amp;
125 make install
126 </action>
127 <action type="set_environment">
128 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
129 </action>
130 </actions>
131 </install>
132 </package-->
133
134 </tool_dependency>