mixcr

#!/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 $?