Mercurial > repos > big-tiandm > sirna_plant

comparison tool_dependencies.xml @ 9:e885b3d4444e draft

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author big-tiandm
date Wed, 29 Oct 2014 04:18:03 -0400
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8:d317cee86d4b 9:e885b3d4444e
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="2.11.0">
13 <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
14 <install version="1.0">
15 <actions>
16 <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
17 </actions>
18 </install>
19 </package>
20
21 <package name="libx11" version="1.5.0">
22 <repositoty name="package_libx11_1_5_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
23 </package>
24
25
26 <package name="threads" version="1.96">
27 <install version="1.0">
28 <actions>
29 <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
30 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
31 <action type="shell_command">make</action>
32 <action type="shell_command">make install</action>
33 <action type="set_environment">
34 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
35 </action>
36 </actions>
37 </install>
38 </package>
39
40
41 <package name="Parallel-ForkManager" version="1.06">
42 <install version="1.0">
43 <actions>
44 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
45 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
46 <action type="shell_command">make</action>
47 <action type="shell_command">make install</action>
48 <action type="set_environment">
49 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
50 </action>
51 </actions>
52 </install>
53 </package>
54
55 <package name="SVG" version="2.59">
56 <install version="1.0">
57 <actions>
58 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
59 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
60 <action type="shell_command">make</action>
61 <action type="shell_command">make install</action>
62 <action type="set_environment">
63 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
64 </action>
65 </actions>
66 </install>
67 </package>
68
69 <package name="Boost-Graph" version="1.4">
70 <install version="1.0">
71 <actions>
72 <action type="download_by_url">http://www.cpan.org/authors/id/D/DB/DBURDICK/BoostGraph/Boost-Graph-1.4.tar.gz</action>
73 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
74 <action type="shell_command">make</action>
75 <action type="shell_command">make install</action>
76 <action type="set_environment">
77 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
78 </action>
79 </actions>
80 </install>
81 </package>
82
83 </tool_dependency>