annotate tool_dependencies.xml @ 53:f5a2e8308836 draft default tip

Uploaded
author big-tiandm
date Mon, 08 Dec 2014 01:51:16 -0500
parents 7b5a48b972e9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
49
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
1 <?xml version="1.0"?>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
2 <tool_dependency>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
3 <package name="fastx_toolkit" version="0.0.13">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
4 <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
5 </package>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
6 <package name="bowtie" version="0.12.7">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
8 </package>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
9 <set_environment version="1.0">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
10 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
11 </set_environment>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
12 <!--package name="R" version="3.0.1">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
13 <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
14 </package!-->
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
15
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
16 <package name="ViennaRNA" version="2.1.8">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
17 <install version="1.0">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
18 <actions>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
19 <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
20 <action type="shell_command">./configure --prefix=$INSTALL_DIR </action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
21 <action type="shell_command">make</action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
22 <action type="shell_command">make install</action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
23 <action type="set_environment">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
25 </action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
26 </actions>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
27 </install>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
28 </package>
50
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
29 <package name="R" version="3.0.1">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
30 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
31
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
32 <install version="1.0">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
33 <actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
34 <action type="set_environment_for_install">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
35 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
36 <package name="R" version="3.0.1" />
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
37 </repository>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
38 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
39 <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
40 <action type="shell_command">echo "export PATH=$PATH" &gt; $INSTALL_DIR/env.sh </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
41 <action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
42
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
43 </actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
44 </install>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
45 </package>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
46
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
47 <package name="threads" version="1.96">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
48 <install version="1.0">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
49 <actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
50 <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
51 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
52 <action type="shell_command">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
53 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
54 make &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
55 make install
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
56 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
57 <action type="set_environment">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
58 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
59 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
60 </actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
61 </install>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
62 </package>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
63
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
64
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
65 <package name="Parallel-ForkManager" version="1.06">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
66 <install version="1.0">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
67 <actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
68 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
69 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
70 <action type="shell_command">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
71 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
72 make &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
73 make install
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
74 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
75 <action type="set_environment">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
76 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
77 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
78 </actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
79 </install>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
80 </package>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
81
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
82 <package name="Boost-Graph" version="1.4_001">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
83 <install version="1.0">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
84 <actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
85 <action type="download_by_url">http://www.cpan.org/authors/id/D/DU/DUFFEE/Boost-Graph-1.4_001.tar.gz</action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
86 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
87 <action type="shell_command">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
88 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
89 ls &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
90 make &amp;&amp;
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
91 make install
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
92 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
93 <action type="set_environment">
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
94 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
95 </action>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
96 </actions>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
97 </install>
7b5a48b972e9 Uploaded
big-tiandm
parents: 49
diff changeset
98 </package>
49
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
99
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
100 <package name="SVG" version="2.59">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
101 <install version="1.0">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
102 <actions>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
103 <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
104 <action type="make_directory">$INSTALL_DIR/lib/perl5</action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
105 <action type="shell_command">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
106 perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
107 make &amp;&amp;
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
108 make install
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
109 </action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
110 <action type="set_environment">
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
111 <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
112 </action>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
113 </actions>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
114 </install>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
115 </package>
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
116
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
117
f008ab2cadc6 Uploaded
big-tiandm
parents:
diff changeset
118 </tool_dependency>