Mercurial > repos > iuc > package_r_3_0_3
diff tool_dependencies.xml @ 3:a8438aa1207c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_r_3_0_3 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
| author | iuc |
|---|---|
| date | Fri, 17 Jul 2015 10:52:21 -0400 |
| parents | f386d7431fe0 |
| children | afc48696ee5c |
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--- a/tool_dependencies.xml Tue Jun 24 15:47:01 2014 -0400 +++ b/tool_dependencies.xml Fri Jul 17 10:52:21 2015 -0400 @@ -1,59 +1,59 @@ <?xml version="1.0"?> <tool_dependency> - <package name="R" version="3.0.3"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.3-Darwin-x86_64.tgz</action> + <package name="R" version="3.0.3"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.3-Darwin-x86_64.tgz</action> <action type="move_directory_files"> - <source_directory>.</source_directory> + <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="shell_command">sh $INSTALL_DIR/darwin_post_install.sh $INSTALL_DIR</action> </actions> <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.3-Linux-x86_64.tgz</action> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.3-Linux-x86_64.tgz</action> <action type="move_directory_files"> - <source_directory>.</source_directory> + <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="set_environment"> - <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable> + <environment_variable action="set_to" name="TCL_LIBRARY">$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> - <package name="readline" version="6.2"> - <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="readline" version="6.2"> + <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="libpng" version="1.6.7"> - <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="cairo" version="1.12.14"> - <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="pixman" version="0.32.4"> - <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="freetype" version="2.5.2"> - <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.3.tar.gz</action> <action type="set_environment_for_install"> - <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="readline" version="6.2" /> + <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="readline" version="6.2" /> </repository> - <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> + <repository changeset_revision="f48b920cae1f" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> </repository> - <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="cairo" version="1.12.14" /> + <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="cairo" version="1.12.14" /> </repository> - <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="pixman" version="0.32.4" /> + <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.4" /> </repository> - <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.5.2" /> + <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="freetype" version="2.5.2" /> </repository> </action> <action type="shell_command"> @@ -75,22 +75,23 @@ --enable-R-shlib \ --disable-R-framework \ --libdir=$INSTALL_DIR/lib \ - --prefix=$INSTALL_DIR + --prefix=$INSTALL_DIR </action> <action type="make_install" /> - <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action> - <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action> + <action type="shell_command">sed -i.bak -e 's;$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_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="R_HOME">$INSTALL_DIR</environment_variable> <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable> </action> </actions_group> </install>