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mixcr
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#!/usr/bin/env bash
app="mixcr"
defaultXmx=12000
java="java"
sedString1="s/\s*\([^.]*\)\..*/\1/"
sedString2="s/.*1\.\(.*\)\..*/\1/"
jVersion=$($java -version 2>&1 | grep version | awk '{ print $3 }' | sed 's:"::g')
jVersion1=$(echo "$jVersion" | sed $sedString1)
if [[ jVersion1 -eq 1 ]]; then
jVersion2=$(echo "$jVersion" | sed $sedString2)
if [[ $jVersion2 -lt 7 ]]; then
echo "Wrong version of java. Please use Java 7 or higher."
exit 1
fi
if [[ $jVersion2 -lt 8 ]]; then
echo "WARNING: Several issues have been detected while using Java 7. Please consider updateing to Java 8 or higher."
fi
jVersion="$jVersion2"
elif [[ jVersion1 -lt 9 ]]; then
echo "Wrong version of java. Please use Java 7 or higher."
exit 1
else
jVersion="$jVersion1"
fi
# Linux readlink -f alternative for Mac OS X
function readlinkUniversal() {
targetFile=$1
cd $(dirname "$targetFile")
targetFile=$(basename $targetFile)
# iterate down a (possible) chain of symlinks
while [ -L "$targetFile" ]; do
targetFile=$(readlink $targetFile)
cd $(dirname "$targetFile")
targetFile=$(basename $targetFile)
done
# compute the canonicalized name by finding the physical path
# for the directory we're in and appending the target file.
phys_dir=$(pwd -P)
result=$phys_dir/$targetFile
echo "$result"
}
os=$(uname)
delta=100
dir=""
maxMb="???"
function calculateMaxMb() {
case $os in
Darwin)
freeBlocks=$(vm_stat | grep free | awk '{ print $3 }' | sed 's/\.//')
inactiveBlocks=$(vm_stat | grep inactive | awk '{ print $3 }' | sed 's/\.//')
speculativeBlocks=$(vm_stat | grep speculative | awk '{ print $3 }' | sed 's/\.//')
freeMb=$(((freeBlocks + speculativeBlocks) * 4096 / 1048576))
inactiveMb=$((inactiveBlocks * 4096 / 1048576))
maxMb=$(((freeMb + inactiveMb - delta)))
;;
Linux)
# 7 is available
rFreeMb=$(free -m | grep Mem | awk '{ print $7 }')
maxMb=$((rFreeMb - delta))
;;
FreeBSD)
freeBlocks=$(vmstat -s | grep -E 'free$' | awk '{ print $1 }')
inactiveBlocks=$(vmstat -s | grep inactive | awk '{ print $1 }')
freeMb=$(((freeBlocks + inactiveBlocks) * 4096 / 1048576))
maxMb=$((freeMb - delta))
;;
*)
echo "Unknown OS."
exit 1
;;
esac
if [[ -n ${MAX_MEMORY_OVERRIDE+x} ]]; then
maxMb="${MAX_MEMORY_OVERRIDE}"
fi
}
case $os in
Darwin)
dir=$(dirname "$(readlinkUniversal "$0")")
;;
Linux)
dir="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
;;
FreeBSD)
dir=$(dirname "$(readlinkUniversal "$0")")
;;
*)
echo "Unknown OS."
exit 1
;;
esac
appArgs=()
javaArgs=()
needXmxXms=true
altJar=""
inDocker=false
if [[ -f /proc/1/cgroup ]] && grep docker /proc/1/cgroup -qa || [[ -f /.dockerenv ]]; then
inDocker=true
fi
while [[ $# -gt 0 ]]; do
key="$1"
shift
case $key in
-D* | -X* | -ea | -agentlib*)
javaArgs+=("${key}")
case $key in
-Xmx* | -Xms*)
needXmxXms=false
;;
esac
;;
-jar | -V)
altJar="$1"
shift
;;
*)
appArgs+=("${key}")
;;
esac
done
scr=${dir}/scr
if [[ -n ${altJar} ]]; then
scr="${scr} -V ${altJar}"
fi
if [[ ${needXmxXms} == true ]]; then
if [[ ${inDocker} == true ]] && [[ jVersion -ge 11 ]]; then
javaArgs+=("-XX:MaxRAMPercentage=85.0")
else
targetXmx=$defaultXmx
calculateMaxMb
if [[ $targetXmx -gt $maxMb ]]; then
targetXmx=$maxMb
fi
memoryConsumingCommands=("analyze" "refineTagsAndSort" "assemblePartial" "assemble" "findShmTrees" "postanalysis" "downsampling")
needWarn=false
for mcmd in "${memoryConsumingCommands[@]}"; do
if [[ " ${appArgs[*]} " =~ ${mcmd} ]]; then
needWarn=true
break
fi
done
if [[ ${needWarn} == true ]]; then
echo "IMPORTANT: MiXCR will use at most ${targetXmx}MB of RAM," >&2
echo " use -Xmx to change automatically set heap size (i.e. -Xmx50g to set heap size to 50 Gb)" >&2
fi
javaArgs+=("-Xmx${targetXmx}m")
targetXms=$((targetXmx * 2 / 3))
if [[ $targetXms -lt 2000 ]]; then
targetXms=$targetXmx
fi
if [[ $targetXms -gt 6000 ]]; then
targetXms="6000"
fi
javaArgs+=("-Xms${targetXms}m")
fi
fi
jar=""
if [[ -z "$altJar" ]]; then
for j in "$dir/../jar/${app}.jar" "$dir/${app}.jar" $(ls -d -1 "$dir"/build/libs/* 2>/dev/null | grep "${app}" | grep all.jar); do
if [[ -e "$j" ]]; then
jar=$j
break
fi
done
else
for j in $(ls -1 "${dir}"/* | grep "${app}-${altJar}.jar"); do
if [[ -e "$j" ]]; then
jar=$j
break
fi
done
fi
if [[ "$jar" == "" ]]; then
echo "No jar."
exit 1
fi
$java -Dmi.license.file="$dir/mi.license" -D${app}.path="$dir" -D${app}.command=${app} "${javaArgs[@]}" -jar "$jar" "${appArgs[@]}"
exit $?