Mercurial > repos > deepakjadmin > r_3_2_0_test2

comparison tool_dependencies.xml @ 0:89814339672c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 23 Sep 2015 03:43:12 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:89814339672c
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="R" version="3.2.0">
4 <install version="1.0">
5 <actions_group>
6 <actions architecture="x86_64" os="darwin">
7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <actions architecture="x86_64" os="linux">
14 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR</destination_directory>
18 </action>
19 <action type="set_environment">
20 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
21 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
22 </action>
23 </actions>
24 <actions>
25 <package name="readline" version="6.2">
26 <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
27 </package>
28 <package name="libpng" version="1.6.7">
29 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
30 </package>
31 <package name="cairo" version="1.12.14">
32 <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
33 </package>
34 <package name="pixman" version="0.32.4">
35 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
36 </package>
37 <package name="freetype" version="2.5.2">
38 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
39 </package>
40 <action type="set_environment_for_install">
41 <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
42 <package name="readline" version="6.2" />
43 </repository>
44 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
45 <package name="libpng" version="1.6.7" />
46 </repository>
47 <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
48 <package name="cairo" version="1.12.14" />
49 </repository>
50 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
51 <package name="pixman" version="0.32.4" />
52 </repository>
53 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
54 <package name="freetype" version="2.5.2" />
55 </repository>
56 </action>
57 <action type="shell_command">
58 export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIBS" &amp;&amp;
59 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIBS" &amp;&amp;
60 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
61 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
62 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
63 export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &amp;&amp;
64 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &amp;&amp;
65 export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &amp;&amp;
66 ./configure --with-tcltk \
67 --with-blas \
68 --with-lapack \
69 --with-readline \
70 --with-cairo \
71 --with-libpng \
72 --without-x \
73 --enable-R-shlib \
74 --disable-R-framework \
75 --libdir=$INSTALL_DIR/lib \
76 --prefix=$INSTALL_DIR
77 </action>
78 <action type="make_install" />
79 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
80 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
81 </actions>
82 <action type="set_environment">
83 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
84 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
85 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
86 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
87 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
88 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
89 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
90 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
92 </action>
93 </actions_group>
94 </install>
95 <readme>
96 The precompiled versions of this package were built 2014-03-06.
97 R is a free software environment for statistical computing and graphics.
98 NOTE: See custom compilation options above.
99 </readme>
100 </package>
101
102 <package name="limma" version="3.24.15">
103 <install version="1.0">
104 <actions>
105 <action type="setup_r_environment">
106 <package name="R" version="3.2.0">
107 <repository changeset_revision="17cf1bdcf41f" name="r_3_2_0_test1" owner="deepakjadmin" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
108 </package>
109 <action type="download_by_url">http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.15.tar.gz</action>
110 <action type="shell_command">R CMD INSTALL tar.gz</action>
111 </action>
112 </actions>
113 </install>
114 <readme>
115 limma_3.24.12 installed now try edgeR
116 </readme>
117
118 </package>
119
120 </tool_dependency>