Mercurial > repos > s-kaufmann > synteny_mapper
changeset 15:9a495fd2fe0f draft
Uploaded
| author | s-kaufmann |
|---|---|
| date | Fri, 15 Aug 2014 10:19:49 -0400 |
| parents | acb6cae8bfec |
| children | a6af076506eb |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 89 insertions(+), 61 deletions(-) [+] |
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--- a/tool_dependencies.xml Fri Aug 15 09:49:46 2014 -0400 +++ b/tool_dependencies.xml Fri Aug 15 10:19:49 2014 -0400 @@ -1,69 +1,97 @@ <?xml version="1.0"?> <tool_dependency> - <set_environment version="1.0"> - <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - - <set_environment version="1.0"> - <environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - -<package name="circos" version="0.64"> - <install version="1.0"> - <actions> - <!-- Downloads the Circos software from its website and unpacks it --> - <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> -Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed. - </readme> - </package> - - <set_environment version="1.0"> - <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="R_3_0_2" version="3.0.2"> <install version="1.0"> - <actions> - <action type="download_by_url">http://cran.ms.unimelb.edu.au/src/base/R-3/R-3.0.2.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="readline" version="6.2" /> - </repository> - <repository changeset_revision="9ed7af129bd3" name="package_ncurses_5_9" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="ncurses" version="5.9" /> - </repository> - <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="libpng" version="1.6.7" /> - </repository> - </action> - -<action type="shell_command"> - ./configure CPPFLAGS="-I$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=$INSTALL_DIR/share/ + <actions_group> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</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> + <package name="readline" version="6.2"> + <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.6.7"> + <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="cairo" version="1.12.14"> + <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="pixman" version="0.32.4"> + <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="freetype" version="2.5.2"> + <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="readline" version="6.2" /> + </repository> + <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="cairo" version="1.12.14" /> + </repository> + <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="pixman" version="0.32.4" /> + </repository> + <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="freetype" version="2.5.2" /> + </repository> + </action> + <action type="shell_command"> + export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" && + export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && + export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && + export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" && + ./configure --with-tcltk \ + --with-blas \ + --with-lapack \ + --with-readline \ + --with-cairo \ + --with-libpng \ + --without-x \ + --enable-R-shlib \ + --disable-R-framework \ + --libdir=$INSTALL_DIR/lib \ + --prefix=$INSTALL_DIR + </action> + <action type="make_install" /> + <action type="shell_command">sed -i.bak 's;$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' $INSTALL_DIR/lib/R/bin/R</action> + </actions> + <action type="set_environment"> + <environment_variable action="set_to" name="R_ROOT_DIR">$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">$INSTALL_DIR/lib/R/library</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> - - <action type="shell_command">make</action> - <action type="shell_command">make install</action> - <action type="set_environment"> - <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable> - <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/R/lib</environment_variable> - <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_PATH">$INSTALL_DIR/lib/R/bin</environment_variable> - </action> - </actions> + </actions_group> </install> - <readme>R is a free software environment for statistical computing and graphics. http://www.r-project.org/</readme> + <readme> + The precompiled versions were built 2014-03-07. + R is a free software environment for statistical computing and graphics. http://www.r-project.org/ + </readme> </package> - </tool_dependency>