etc/gatk-wdl/fm2gatk/bin/picard.sh

   1 #!/bin/bash
   2 # Picard executable shell script
   3 # https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh
   4 set -eu -o pipefail
   5
   6 export LC_ALL=en_US.UTF-8
   7
   8 # Find original directory of bash script, resolving symlinks
   9 # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
  10 SOURCE="${BASH_SOURCE[0]}"
  11 while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
  12     DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
  13     SOURCE="$(readlink "$SOURCE")"
  14     [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
  15 done
  16 DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
  17
  18 JAR_DIR=$DIR
  19 ENV_PREFIX="$(dirname $(dirname $DIR))"
  20 # Use Java installed with Anaconda to ensure correct version
  21 java="$ENV_PREFIX/bin/java"
  22
  23 # if JAVA_HOME is set (non-empty), use it. Otherwise keep "java"
  24 if [ -n "${JAVA_HOME:=}" ]; then
  25   if [ -e "$JAVA_HOME/bin/java" ]; then
  26       java="$JAVA_HOME/bin/java"
  27   fi
  28 fi
  29
  30 # extract memory and system property Java arguments from the list of provided arguments
  31 # http://java.dzone.com/articles/better-java-shell-script
  32 default_jvm_mem_opts="-Xms512m -Xmx2g"
  33 jvm_mem_opts=""
  34 jvm_prop_opts=""
  35 pass_args=""
  36 for arg in "$@"; do
  37     case $arg in
  38         '-D'*)
  39             jvm_prop_opts="$jvm_prop_opts $arg"
  40             ;;
  41         '-XX'*)
  42             jvm_prop_opts="$jvm_prop_opts $arg"
  43             ;;
  44          '-Xm'*)
  45             jvm_mem_opts="$jvm_mem_opts $arg"
  46             ;;
  47          *)
  48             if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates'
  49                 then
  50                     pass_args="$arg"
  51             else
  52                     pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg
  53             fi
  54             ;;
  55     esac
  56 done
  57
  58 if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]; then
  59     jvm_mem_opts="$default_jvm_mem_opts"
  60 fi
  61
  62 pass_arr=($pass_args)
  63 if [[ ${pass_arr[0]:=} == org* ]]
  64 then
  65     eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/picard.jar" $pass_args
  66 else
  67     eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/picard.jar" $pass_args
  68 fi
  69 exit