|
2
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <set_environment version="1.0">
|
|
|
4 <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
|
|
|
5 </set_environment>
|
|
|
6
|
|
|
7 <set_environment version="1.0">
|
|
|
8 <environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
|
|
|
9 </set_environment>
|
|
|
10
|
|
|
11 <package name="circos" version="0.64">
|
|
|
12 <install version="1.0">
|
|
|
13 <actions>
|
|
|
14 <!-- Downloads the Circos software from its website and unpacks it -->
|
|
|
15 <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
|
|
|
16 <action type="move_directory_files">
|
|
|
17 <source_directory>.</source_directory>
|
|
|
18 <destination_directory>$INSTALL_DIR/</destination_directory>
|
|
|
19 </action>
|
|
|
20 <action type="set_environment">
|
|
|
21 <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
|
|
|
22 </action>
|
|
|
23 </actions>
|
|
|
24 </install>
|
|
|
25 <readme>
|
|
|
26 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
|
|
|
27 </readme>
|
|
10
|
28 </package>
|
|
|
29
|
|
12
|
30 <set_environment version="1.0">
|
|
|
31 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
|
|
|
32 </set_environment>
|
|
|
33 <package name="readline" version="6.2">
|
|
|
34 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
|
|
|
35 </package>
|
|
|
36 <package name="ncurses" version="5.9">
|
|
|
37 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
|
|
|
38 </package>
|
|
|
39 <package name="libpng" version="1.6.7">
|
|
|
40 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
|
|
|
41 </package>
|
|
|
42 <package name="R_3_0_2" version="3.0.2">
|
|
10
|
43 <install version="1.0">
|
|
|
44 <actions>
|
|
12
|
45 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
|
|
|
46 <action type="set_environment_for_install">
|
|
|
47 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
|
|
10
|
48 <package name="readline" version="6.2" />
|
|
|
49 </repository>
|
|
12
|
50 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
|
|
|
51 <package name="ncurses" version="5.9" />
|
|
|
52 </repository>
|
|
|
53 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
|
|
|
54 <package name="libpng" version="1.6.7" />
|
|
|
55 </repository>
|
|
|
56 </action>
|
|
10
|
57
|
|
12
|
58 <action type="shell_command">
|
|
|
59 ./configure CPPFLAGS="-I$READLINE_INCLUDE_PATH -I${LIBPNG_ROOT}/include" LDFLAGS="-L$READLINE_LIB_PATH -L$NCURSES_LIB_PATH -L${LIBPNG_ROOT}/lib -lreadline -lncurses" --with-libpng --enable-R-shlib --with-x=no --libdir=$INSTALL_DIR/lib/ --bindir=$INSTALL_DIR --datarootdir=$INSTALL_DIR/share/
|
|
10
|
60 </action>
|
|
12
|
61
|
|
10
|
62 <action type="shell_command">make</action>
|
|
|
63 <action type="shell_command">make install</action>
|
|
|
64 <action type="set_environment">
|
|
|
65 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
|
|
|
66 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
|
|
|
67 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
|
|
|
68 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
|
|
|
69 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
|
|
|
70 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
|
|
|
71 </action>
|
|
|
72 </actions>
|
|
|
73 </install>
|
|
|
74 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
|
|
12
|
75 </package>
|
|
2
|
76
|
|
|
77 </tool_dependency>
|
