Mercurial > repos > big-tiandm > sirna_plant

comparison tool_dependencies.xml @ 18:22d79320085c draft

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author big-tiandm
date Thu, 30 Oct 2014 21:31:55 -0400
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children 095812dc2ed9
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17:b75750b21aa4 18:22d79320085c
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 changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
14 </package>
15
16 <package name="degseq" version="1.20.0">
17 <install version="1.0">
18 <actions>
19 <action type="set_environment_for_install">
20 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
21 <package name="R" version="3.0.1" />
22 </repository>
23 </action>
24 <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
25 </actions>
26 </install>
27 </package>
28
29 <package name="threads" version="1.96">
30 <install version="1.0">
31 <actions>
32 <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
33 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
34 <action type="shell_command">make</action>
35 <action type="shell_command">make install</action>
36 <action type="set_environment">
37 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
38 </action>
39 </actions>
40 </install>
41 </package>
42
43
44 <package name="Parallel-ForkManager" version="1.06">
45 <install version="1.0">
46 <actions>
47 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
48 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
49 <action type="shell_command">make</action>
50 <action type="shell_command">make install</action>
51 <action type="set_environment">
52 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
53 </action>
54 </actions>
55 </install>
56 </package>
57
58 <package name="SVG" version="2.59">
59 <install version="1.0">
60 <actions>
61 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
62 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
63 <action type="shell_command">make</action>
64 <action type="shell_command">make install</action>
65 <action type="set_environment">
66 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
67 </action>
68 </actions>
69 </install>
70 </package>
71
72 <package name="Boost-Graph" version="1.4">
73 <install version="1.0">
74 <actions>
75 <action type="download_by_url">http://www.cpan.org/authors/id/D/DB/DBURDICK/BoostGraph/Boost-Graph-1.4.tar.gz</action>
76 <action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR </action>
77 <action type="shell_command">make</action>
78 <action type="shell_command">make install</action>
79 <action type="set_environment">
80 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib</environment_variable>
81 </action>
82 </actions>
83 </install>
84 </package>
85
86 </tool_dependency>