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# | |
# set these values in your GP_HOME/custom.properties file | |
# | |
# | |
# the wrapper scripts are in the resources directory | |
# | |
wrapper-scripts=<resources>/wrapper_scripts | |
run-with-env=<wrapper-scripts>/run-with-env.sh -c <env-custom> | |
rjava_flags=-Xmx512m | |
python_2.5=<run-with-env> -u Python-2.5 python | |
python_2.6=<run-with-env> -u Python-2.6 python | |
python_2.7=<run-with-env> -u Python-2.7 python | |
run-rjava=<wrapper-scripts>/run-rjava.sh -c <env-custom> | |
R2.0_Rjava=<run-rjava> 2.0 <rjava_flags> -cp <run_r_path> RunR | |
R=<R2.0_Rjava> | |
R2.5_Rjava=<run-rjava> 2.5 <rjava_flags> -cp <run_r_path> RunR | |
R2.5_Rscript=<run-with-env> -u R-2.5 Rscript | |
R2.5=<R2.5_Rjava> | |
R2.7_Rjava=<run-rjava> 2.7 <rjava_flags> -cp <run_r_path> RunR | |
R2.7_Rscript=<run-with-env> -u R-2.7 Rscript | |
R2.7=<R2.7_Rjava> | |
R-2.7.2=<R2.7_Rjava> | |
R2.10_Rjava=<run-rjava> 2.10 <rjava_flags> -cp <run_r_path> RunR | |
R2.10_Rscript=<run-with-env> -u R-2.10 Rscript | |
R2.10=<R2.10_Rjava> | |
R2.11_Rjava=<run-rjava> 2.11 <rjava_flags> -cp <run_r_path> RunR | |
R2.11_Rscript=<run-with-env> -u R-2.11 Rscript | |
R2.11=<R2.11_Rjava> | |
R2.13_Rjava=<run-rjava> 2.13 <rjava_flags> -cp <run_r_path> RunR | |
R2.13_Rscript=<run-with-env> -u R-2.13 Rscript | |
R2.13=<R2.13_Rjava> | |
R2.14_Rjava=<run-rjava> 2.14 <rjava_flags> -cp <run_r_path> RunR | |
R2.14=<R2.14_Rjava> | |
R2.15_Rjava=<run-rjava> 2.15 <rjava_flags> -cp <run_r_path> RunR | |
# Rscript wrapper command, updated in GP 3.9.10 | |
# see: https://stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html | |
# see: https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html | |
# see: https://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html | |
env.GP_R_LIBS_SITE_PREFIX=<patches>/Library/R | |
env.GP_R_LIBS_SITE= | |
job.env.GP_DEBUG=false | |
job.env.GP_DRY_RUN=false | |
# R Package Installer configuration | |
job.env.GP_R_PACKAGE_INFO=<libdir>r.package.info | |
job.env.GP_INSTALL_PACKAGES_OUT=.install.packages.out | |
job.env.GP_INSTALL_PACKAGES_LOG=.install.packages.log | |
run-rscript-cmd=<wrapper-scripts>/run-rscript-pkgs.sh | |
run-rscript-args=-c env-custom-macos.sh \ | |
-e GP_R_LIBS_SITE_PREFIX=<env.GP_R_LIBS_SITE_PREFIX> \ | |
-e GP_R_LIBS_SITE=<env.GP_R_LIBS_SITE> \ | |
-e GP_R_PACKAGE_INFO=<job.env.GP_R_PACKAGE_INFO> \ | |
-e GP_DRY_RUN=<job.env.GP_DRY_RUN> \ | |
-e GP_DEBUG=<job.env.GP_DEBUG> \ | |
-e GP_INSTALL_PACKAGES_OUT=<job.env.GP_INSTALL_PACKAGES_OUT> \ | |
-e GP_INSTALL_PACKAGES_LOG=<job.env.GP_INSTALL_PACKAGES_LOG> \ | |
-- | |
R2.14_Rscript=<run-rscript-cmd> -v 2.14 <run-rscript-args> | |
R2.15_Rscript=<run-rscript-cmd> -v 2.15 <run-rscript-args> | |
R3.0_Rscript=<run-rscript-cmd> -v 3.0 <run-rscript-args> | |
R3.1_Rscript=<run-rscript-cmd> -v 3.1 <run-rscript-args> | |
R3.2_Rscript=<run-rscript> -v 3.2 -- | |
R3.3_Rscript=<run-rscript-cmd> -v 3.3 <run-rscript-args> | |
# | |
# Some legacy modules require 'R2.14_HOME' and 'R2.15_HOME' | |
# to be set to an installation specific path | |
#R2.14_HOME= | |
#R2.15_HOME= | |
# | |
# Rscript wrapper commands from GP <= 3.9.9 | |
# | |
# run-rscript=<wrapper-scripts>/run-rscript.sh -c <env-custom> -a <env-arch> -l <libdir> -p <patches> | |
# R2.14_Rscript=<run-rscript> -v 2.14 -- | |
# R2.15_Rscript=<run-rscript> -v 2.15 -- | |
# R3.0_Rscript=<run-rscript> -v 3.0 -- | |
# R3.1_Rscript=<run-rscript> -v 3.1 -- | |
# R3.2_Rscript=<run-rscript> -v 3.2 -- | |
# | |
# Note: Multi-arg java command is problematic for java modules (circa GP 3.9.6/3.9.7) | |
# java=<run-with-env> -u Java java <---- don't do this | |
# Instead you must set java to the fully qualified path to the java executable | |
# For example, | |
# java-1.7-centos5-path=/opt/software/centos_5_x86_64/pkgs/oracle-java-jdk_1.7.0-51_x86_64/bin/java | |
# java-1.7-rhel6-path=/opt/software/rhel_6_x86_65/pkgs/oracle-java-jdk_1.7.0-51_x86_64/bin/java | |
# java-cmd=<java-1.7-centos5-path> | |
# Default values work out-of-the-box on Mac OS X | |
java=<java-cmd> | |
java-cmd=java | |
java-with-env=<run-with-env> -u Java java | |
# by default, use system configured perl command | |
perl=<perl-cmd> | |
perl-cmd=perl | |
perl-with-env=<run-with-env> -u Perl perl | |
perl_5.10=<run-with-env> -u Perl-5.10 perl | |