Mercurial > repos > iuc > package_r_3_2_1

comparison tool_dependencies.xml @ 0:e46a7803f17b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 1ddb71f5953e86441c06326980abd33168087e50
author iuc
date Mon, 21 Sep 2015 10:22:04 -0400
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children fae49a02a848
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-1:000000000000 0:e46a7803f17b
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="R" version="3.2.1">
4 <install version="1.0">
5 <actions_group>
6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 <action type="set_environment">
13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
15 </action>
16 </actions>
17 <actions>
18 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action>
19 <package name="atlas" version="3.10.2">
20 <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
21 </package>
22 <package name="readline" version="6.3">
23 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
24 </package>
25 <package name="libpng" version="1.6.7">
26 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
27 </package>
28 <package name="cairo" version="1.12.14">
29 <repository changeset_revision="84c45dea6b9e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
30 </package>
31 <package name="pixman" version="0.32.6">
32 <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
33 </package>
34 <package name="freetype" version="2.5.2">
35 <repository changeset_revision="831c84793e0f" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
36 </package>
37 <package name="ncurses" version="6.0">
38 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
39 </package>
40 <package name="fontconfig" version="2.11.1">
41 <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
42 </package>
43 <action type="set_environment_for_install">
44 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
45 <package name="readline" version="6.3" />
46 </repository>
47 <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
48 <package name="libpng" version="1.6.7" />
49 </repository>
50 <repository changeset_revision="84c45dea6b9e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
51 <package name="cairo" version="1.12.14" />
52 </repository>
53 <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
54 <package name="pixman" version="0.32.6" />
55 </repository>
56 <repository changeset_revision="831c84793e0f" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
57 <package name="freetype" version="2.5.2" />
58 </repository>
59 <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
60 <package name="ncurses" version="6.0" />
61 </repository>
62 <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
63 <package name="fontconfig" version="2.11.1" />
64 </repository>
65 </action>
66 <action type="shell_command">
67 export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" &amp;&amp;
68 export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" &amp;&amp;
69 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
70 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
71 export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" &amp;&amp;
72 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
73 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" &amp;&amp;
74 export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" &amp;&amp;
75 export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
76 export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
77 export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" &amp;&amp;
78 ./configure --with-tcltk \
79 --with-blas \
80 --with-lapack \
81 --with-readline \
82 --with-cairo \
83 --with-libpng \
84 --without-x \
85 --enable-R-shlib \
86 --disable-R-framework \
87 --libdir=$INSTALL_DIR/lib \
88 --prefix=$INSTALL_DIR
89 </action>
90 <action type="make_install" />
91 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
92 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
93 </actions>
94 <action type="set_environment">
95 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
96 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
97 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
98 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
99 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
100 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
101 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
102 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
103 <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
104 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
105 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
106 </action>
107 </actions_group>
108 </install>
109 <readme>
110 The precompiled versions of this package were built 2015-07-27.
111 R is a free software environment for statistical computing and graphics.
112 NOTE: See custom compilation options above.
113 </readme>
114 </package>
115 </tool_dependency>