Mercurial > repos > deepakjadmin > r_3_2_0_test3
changeset 0:6ce3b057cf50 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 23 Sep 2015 03:48:30 -0400 |
| parents | |
| children | |
| files | testing.xml tool_dependencies.xml |
| diffstat | 2 files changed, 135 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/testing.xml Wed Sep 23 03:48:30 2015 -0400 @@ -0,0 +1,15 @@ +<tool id="k1cv02rt90uis" name="R-3-2-0 test2" version="1.0.0"> + <description>R version and installation test</description> +<requirements> + <requirement type="set_environment">R_ROOT_DIR</requirement> + <requirement type="package" version="3.2.0">R</requirement> +</requirements> + <command> /bin/which R > $output_file; + /bin/which \$R_ROOT_DIR/bin/R >> $output_file; + echo \$R_ROOT_DIR >> $output_file; + echo \$PATH >> $output_file; + </command> + <outputs> + <data type="data" format="txt" name="output_file" label ="output_r_3_2_0.env" /> + </outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 23 03:48:30 2015 -0400 @@ -0,0 +1,120 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.0"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-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> + <package name="readline" version="6.2"> + <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" 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="8f011e7388e1" 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="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <action type="set_environment_for_install"> + <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" 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="8f011e7388e1" 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="34ebf47e4941" 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$READLINE_LIBS" && + export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIBS" && + export LDFLAGS="$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$READLINE_INCLUDES" && + export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" && + export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" && + ./configure --with-tcltk \ + --with-blas \ + --with-lapack \ + --with-readline \ + --with-cairo \ + --with-libpng \ + --without-x \ + --enable-R-shlib \ + --disable-R-framework \ + --libdir=$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' $INSTALL_DIR/lib/R/bin/R</action> + </actions> + <action type="set_environment"> + <environment_variable action="set_to" name="R_DOC_DIR">$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">$INSTALL_DIR/lib/R/library</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme> + The precompiled versions of this package were built 2014-03-06. + R is a free software environment for statistical computing and graphics. + NOTE: See custom compilation options above. + </readme> + </package> + + <package name="limma" version="3.24.15"> + <install version="1.0"> + <actions> + <action type="setup_r_environment"> + <package name="R" version="3.2.0"> + <repository name="r_3_2_0_test2" owner="deepakjadmin" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <action type="download_by_url">http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.15.tar.gz</action> + <action type="shell_command">R CMD INSTALL limma_3.24.15.tar.gz</action> + </action> + </actions> + </install> + <readme> +limma_3.24.12 installed now try edgeR + </readme> + + </package> + +</tool_dependency>