G'day,
I'm finishing off a module that uses an R package to perform baseline
correction of raw data files.
I want to know how to best package this module given that it introduces
a dependency on R and some R packages. In order for the module to work
the system needs:
1. R installed (64-bit if 64-bit JRE is running MZmine 2)
2. rJava package installed in R
3. ptw package installed in R
Then the following lines need to be added/changed in startMZmine_Linux.sh:
# Set R environment variables.
export R_HOME=/usr/lib64/R
export R_SHARE_DIR=/usr/share/R/share
export R_INCLUDE_DIR=/usr/share/R/include
export R_DOC_DIR=/usr/share/R/doc
export LD_LIBRARY_PATH=${R_HOME}/lib:${R_HOME}/bin
# Set JRI path: the directory holding the JRI JAR files and library.
JRI_PATH=${HOME}/R/x86_64-pc-linux-gnu-library/2.10/rJava/jri
# It is not necessary to modify the following section
LOGGING_CONFIG_FILE=conf/logging.properties
JAVA_PARAMETERS="-XX:+UseParallelGC -Djava.io.tmpdir=$TMP_FILE_DIRECTORY
-Djava.util.logging.config.file=$LOGGING_CONFIG_FILE $USE_64_BIT
-Xms${HEAP_SIZE}m -Xmx${HEAP_SIZE}m -Djava.library.path=${JRI_PATH}"
CLASS_PATH=MZmine2.jar:${JRI_PATH}/JRIEngine.jar:${JRI_PATH}/JRI.jar:${JRI_PATH}/REngine.jar
(similarly for Windows and MacOS).
In fact, I've created separate start scripts rather than mess with the
originals. Is this neat enough for contribution?
Regards,
Chris.
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Registered Office : Syngenta Limited, European Regional Centre, Priestley Road,
Surrey Research Park, Guildford, Surrey, GU2 7YH, United Kingdom
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