nf-test

#!/usr/bin/env bash
APP_HOME="$HOME/.nf-test"
APP_JAR="nf-test.jar"
APP_UPDATE_URL="https://code.askimed.com/install/nf-test"

set -e

FOLDER=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )

update() {
  if command -v curl > /dev/null 2>&1; then
    curl -fsSL ${APP_UPDATE_URL} | bash
  else
    wget -qO- ${APP_UPDATE_URL} | bash
  fi
}

# nf-test uses the same logic as Nextflow to ensure to pick up the same jvm.
# https://github.com/nextflow-io/nextflow/blob/master/nextflow#L263
if [[ "$NXF_JAVA_HOME" ]]; then
  JAVA_HOME="$NXF_JAVA_HOME"
  unset JAVA_CMD
fi
# Determine the Java command to use to start the JVM.
if [ ! -x "$JAVA_CMD" ] ; then
    if [ -d "$JAVA_HOME" ] ; then
        if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
            # IBM's JDK on AIX uses strange locations for the executables
            JAVA_CMD="$JAVA_HOME/jre/sh/java"
        else
            JAVA_CMD="$JAVA_HOME/bin/java"
        fi
    elif [ -x /usr/libexec/java_home ]; then
        JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java"
    else
        JAVA_CMD="$(which java)" || JAVA_CMD=java
    fi
fi

if test -f "${FOLDER}/${APP_JAR}"; then
  FILE_PATH_JAR=${FOLDER}/${APP_JAR}
else
  FILE_PATH_JAR=${APP_HOME}/${APP_JAR}
fi

JAVA_ARGS="-Xmx10G"
if [[ "$NFT_JAVA_ARGS" ]]; then
  JAVA_ARGS="$NFT_JAVA_ARGS"
fi

export JAVA_PROGRAM_ARGS=`echo "$@"`

if [ "${JAVA_PROGRAM_ARGS}" = "update" ]; then
  echo "Updating application..."
  cd "${FOLDER}"
  update
else
  exec ${JAVA_CMD} ${JAVA_ARGS} -jar "${FILE_PATH_JAR}" "$@"
fi