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BEAST: Difference between revisions
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fix usage of beagle-lb
(Add location of Beagle to LD_LIBRARY_PATH) |
(fix usage of beagle-lb) |
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| Line 74: | Line 74: | ||
#SBATCH --account=def-someuser | #SBATCH --account=def-someuser | ||
#SBATCH --time=3:00:00 | #SBATCH --time=3:00:00 | ||
#SBATCH --mem=4000M | #SBATCH --mem-per-cpu=4000M | ||
# Increase Maximum memory here if necessary: | # Increase Maximum memory here if necessary: | ||
| Line 80: | Line 80: | ||
BEAST_MEM="-Xmx3750M" | BEAST_MEM="-Xmx3750M" | ||
module load beast/2. | module load beast/2.5.1 | ||
# Define a shorter variable where to find BEAST | # Define a shorter variable where to find BEAST | ||
BEAST_LIB="${EBROOTBEAST}/lib" | |||
# use BEAST_EXTRA_LIBS variable to load BEAGLE and other | |||
# libraries from non-default locations | |||
BEAST_EXTRA_LIBS="${BEAST_LIB}:${BEAGLE_LIB}" | |||
# Add location of Beagle to LD_LIBRARY_PATH: | # Add location of Beagle to LD_LIBRARY_PATH: | ||
| Line 89: | Line 93: | ||
# Build a long java command: | # Build a long java command: | ||
CMD="java -Xms256m ${BEAST_MEM}" | CMD="java -Xms256m ${BEAST_MEM}" # set memory | ||
CMD="$CMD -Djava.library.path=${ | CMD="$CMD -Djava.library.path=${BEAST_EXTRA_LIBS}" # point to libraries | ||
CMD="$CMD -jar ${ | CMD="$CMD -jar ${BEAST_LIB}/beast.jar" # which program to execute | ||
echo ".................................." | echo ".................................." | ||
| Line 98: | Line 102: | ||
# Run the command: | # Run the command: | ||
$CMD input_beast.xml | $CMD -beagle input_beast.xml | ||
}} | }} | ||