|
18
|
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 $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
|
|
|
25 </actions>
|
|
|
26 </install>
|
|
|
27 </package>
|
|
|
28
|
|
|
29 <package name="threads" version="1.96">
|
|
|
30 <install version="1.0">
|
|
|
31 <actions>
|
|
|
32 <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
|
|
26
|
33 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
|
|
|
34 <action type="shell_command">
|
|
|
35 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
|
|
|
36 make &&
|
|
|
37 make install
|
|
|
38 </action>
|
|
|
39 <action type="set_environment">
|
|
27
|
40 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
|
|
26
|
41 </action>
|
|
18
|
42 </actions>
|
|
|
43 </install>
|
|
|
44 </package>
|
|
|
45
|
|
|
46
|
|
|
47 <package name="Parallel-ForkManager" version="1.06">
|
|
|
48 <install version="1.0">
|
|
|
49 <actions>
|
|
|
50 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
|
|
26
|
51 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
|
|
|
52 <action type="shell_command">
|
|
|
53 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
|
|
|
54 make &&
|
|
|
55 make install
|
|
|
56 </action>
|
|
|
57 <action type="set_environment">
|
|
27
|
58 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
|
|
26
|
59 </action>
|
|
18
|
60 </actions>
|
|
|
61 </install>
|
|
|
62 </package>
|
|
|
63
|
|
|
64 <package name="SVG" version="2.59">
|
|
|
65 <install version="1.0">
|
|
|
66 <actions>
|
|
|
67 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
|
|
26
|
68 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
|
|
|
69 <action type="shell_command">
|
|
|
70 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
|
|
|
71 make &&
|
|
|
72 make install
|
|
|
73 </action>
|
|
|
74 <action type="set_environment">
|
|
27
|
75 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
|
|
26
|
76 </action>
|
|
18
|
77 </actions>
|
|
|
78 </install>
|
|
|
79 </package>
|
|
|
80
|
|
|
81 <package name="Boost-Graph" version="1.4">
|
|
|
82 <install version="1.0">
|
|
|
83 <actions>
|
|
|
84 <action type="download_by_url">http://www.cpan.org/authors/id/D/DB/DBURDICK/BoostGraph/Boost-Graph-1.4.tar.gz</action>
|
|
26
|
85 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
|
|
|
86 <action type="shell_command">
|
|
|
87 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &&
|
|
28
|
88 ls &&
|
|
26
|
89 make &&
|
|
|
90 make install
|
|
|
91 </action>
|
|
|
92 <action type="set_environment">
|
|
27
|
93 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
|
|
26
|
94 </action>
|
|
18
|
95 </actions>
|
|
|
96 </install>
|
|
|
97 </package>
|
|
|
98
|
|
|
99 </tool_dependency>
|
