Mercurial > repos > s-kaufmann > synteny_mapper

comparison tool_dependencies.xml @ 22:9914e0ec5a31 draft

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author s-kaufmann
date Fri, 15 Aug 2014 11:26:45 -0400
parents 3208b7066844
children 37f25cf20a52
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21:3208b7066844 22:9914e0ec5a31
30 30
31 <set_environment version="1.0"> 31 <set_environment version="1.0">
32 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> 32 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
33 </set_environment> 33 </set_environment>
34 34
35 <package name="R_3_0_2" version="3.0.2"> 35 <package name="R_3_0_2" version="3.0.2">
36 <install version="1.0"> 36 <install version="1.0">
37 <actions_group> 37 <actions>
38 <actions architecture="x86_64" os="darwin"> 38 <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action>
39 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action> 39 <action type="set_environment_for_install">
40 <action type="move_directory_files"> 40 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
41 <source_directory>.</source_directory> 41 <package name="readline" version="6.2" />
42 <destination_directory>$INSTALL_DIR</destination_directory> 42 </repository>
43 </action> 43 <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
44 </actions> 44 <package name="ncurses" version="5.9" />
45 <actions architecture="x86_64" os="linux"> 45 </repository>
46 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action> 46 <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
47 <action type="move_directory_files"> 47 <package name="libpng" version="1.6.7" />
48 <source_directory>.</source_directory> 48 </repository>
49 <destination_directory>$INSTALL_DIR</destination_directory> 49 </action>
50 </action> 50
51 <action type="set_environment"> 51 <action type="shell_command">
52 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> 52 ./configure CPPFLAGS="-I$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=$INSTALL_DIR/share/
53 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> 53 </action>
54 </action> 54
55 </actions> 55 <action type="shell_command">make</action>
56 <actions> 56 <action type="shell_command">make install</action>
57 <package name="readline" version="6.2">
58 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
59 </package>
60 <package name="libpng" version="1.6.7">
61 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
62 </package>
63 <package name="cairo" version="1.12.14">
64 <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
65 </package>
66 <package name="pixman" version="0.32.4">
67 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
68 </package>
69 <package name="freetype" version="2.5.2">
70 <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
71 </package>
72 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
73 <action type="set_environment_for_install">
74 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
75 <package name="readline" version="6.2" />
76 </repository>
77 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
78 <package name="libpng" version="1.6.7" />
79 </repository>
80 <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
81 <package name="cairo" version="1.12.14" />
82 </repository>
83 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
84 <package name="pixman" version="0.32.4" />
85 </repository>
86 <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
87 <package name="freetype" version="2.5.2" />
88 </repository>
89 </action>
90 <action type="shell_command">
91 export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &amp;&amp;
92 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &amp;&amp;
93 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &amp;&amp;
94 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &amp;&amp;
95 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &amp;&amp;
96 export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
97 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
98 export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &amp;&amp;
99 ./configure --with-tcltk \
100 --with-blas \
101 --with-lapack \
102 --with-readline \
103 --with-cairo \
104 --with-libpng \
105 --without-x \
106 --enable-R-shlib \
107 --disable-R-framework \
108 --libdir=$INSTALL_DIR/lib \
109 --prefix=$INSTALL_DIR
110 </action>
111 <action type="make_install" />
112 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
113 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
114 </actions>
115 <action type="set_environment"> 57 <action type="set_environment">
116 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
117 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> 58 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
59 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
60 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
61 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable>
118 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> 62 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
119 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> 63 <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
120 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
121 </action> 64 </action>
122 </actions_group> 65 </actions>
123 </install> 66 </install>
124 <readme> 67 <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme>
125 The precompiled versions were built 2014-03-07.
126 R is a free software environment for statistical computing and graphics. http://www.r-project.org/
127 </readme>
128 </package> 68 </package>
129 69
130 </tool_dependency> 70 </tool_dependency>