Mercurial > repos > iuc > package_r_3_2_1
view tool_dependencies.xml @ 2:2ce7fd67f394 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_2_1 commit 6eaf4336ff90294e503dedf930ccbe31f8b4efe9
| author | iuc |
|---|---|
| date | Thu, 03 Dec 2015 07:23:45 -0500 |
| parents | fae49a02a848 |
| children | d0bf97420fb5 |
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<?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>$INSTALL_DIR</destination_directory> </action> <action type="shell_command"> command -v gfortran || return 0 BUNDLED_LGF_CANON=$INSTALL_DIR/lib/libgfortran.so.3.0.0 && BUNDLED_LGF_FQSO=$INSTALL_DIR/lib/libgfortran.so.3 && BUNDLED_LGF_VERS=`objdump -p $BUNDLED_LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && echo 'program test; end program test' > test.f90 && gfortran -o test test.f90 && LGF=`ldd test | grep libgfortran | awk '{print $3}'` && LGF_CANON=`readlink -f $LGF` && LGF_VERS=`objdump -p $LGF_CANON | grep GFORTRAN_1 | sed -r 's/.*GFORTRAN_1\.([0-9])+/\1/' | sort -n | tail -1` && if [ $LGF_VERS -gt $BUNDLED_LGF_VERS ]; then cp -p $BUNDLED_LGF_CANON ${BUNDLED_LGF_CANON}.bundled && cp -p $BUNDLED_LGF_FQSO ${BUNDLED_LGF_FQSO}.bundled && cp -p $LGF_CANON $BUNDLED_LGF_CANON && cp -p $LGF_CANON $BUNDLED_LGF_FQSO fi </action> <action type="set_environment"> <environment_variable action="set_to" name="TCL_LIBRARY">$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="3d4edf152b1b" 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="06f701aa92e2" 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="3b09e7916896" 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="2ce32675340e" 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="3d4edf152b1b" 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="06f701aa92e2" 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="3b09e7916896" 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="2ce32675340e" 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="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</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">$INSTALL_DIR/lib/R/library</environment_variable> <environment_variable action="prepend_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable> <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$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>