Mercurial > repos > iuc > package_r_3_2_1
changeset 0:e46a7803f17b draft
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 |
| parents | |
| children | fae49a02a848 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 115 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Sep 21 10:22:04 2015 -0400 @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.1"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> + <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable> + </action> + </actions> + <actions> + <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.2.1.tar.gz</action> + <package name="atlas" version="3.10.2"> + <repository changeset_revision="0538fd672119" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="readline" version="6.3"> + <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="cairo" version="1.12.14"> + <repository changeset_revision="84c45dea6b9e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pixman" version="0.32.6"> + <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <repository changeset_revision="831c84793e0f" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ncurses" version="6.0"> + <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="fontconfig" version="2.11.1"> + <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <action type="set_environment_for_install"> + <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="readline" version="6.3" /> + </repository> + <repository changeset_revision="05df724aefbb" name="package_libpng_1_6_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + <repository changeset_revision="84c45dea6b9e" name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="cairo" version="1.12.14" /> + </repository> + <repository changeset_revision="b67e27ea8bd3" name="package_pixman_0_32_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.6" /> + </repository> + <repository changeset_revision="831c84793e0f" name="package_freetype_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="freetype" version="2.5.2" /> + </repository> + <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncurses" version="6.0" /> + </repository> + <repository changeset_revision="b20e4c53891e" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="fontconfig" version="2.11.1" /> + </repository> + </action> + <action type="shell_command"> + export LDFLAGS="-L$LIBPNG_LIB_PATH -L$PNG_LIBS -L$NCURSES_LIB_PATH -L$READLINE_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$NCURSES_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$LIBPNG_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$FONTCONFIG_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$CAIRO_LIB_PATH" && + export CFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" && + export CXXFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" && + export CPPFLAGS="-I$PNG_INCLUDES -I$NCURSES_INCLUDE_PATH -I$READLINE_INCLUDE_PATH -I$LIBPNG_INCLUDE_PATH -I$FONTCONFIG_INCLUDE_PATH -I$CAIRO_INCLUDE_PATH" && + ./configure --with-tcltk \ + --with-blas \ + --with-lapack \ + --with-readline \ + --with-cairo \ + --with-libpng \ + --without-x \ + --enable-R-shlib \ + --disable-R-framework \ + --libdir=$INSTALL_DIR/lib \ + --prefix=$INSTALL_DIR + </action> + <action type="make_install" /> + <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> + <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> + </actions> + <action type="set_environment"> + <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable> + <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable> + <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable> + <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable> + <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable> + <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> + <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> + <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> + <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> + <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme> + The precompiled versions of this package were built 2015-07-27. + R is a free software environment for statistical computing and graphics. + NOTE: See custom compilation options above. + </readme> + </package> +</tool_dependency>