#!/usr/bin/env bash
+declare -a ARGS=("${@}")
ARG1=$1
-WDIR="$( pwd )"
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
-# check to see if $1 is set and is not start of other cli set args
-OPEN=""
-if [ -n "$ARG1" -a "$ARG1" = "${ARG1#-}" -a \! "$ARG1" = "open" ]; then
- # first argument exists and does not start with a "-" and is not "open"
- OPEN="-open"
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+ ISMACOS=1
fi
-APPDIR="${DIR}"
-JAVA="${APPDIR}/jre/bin/java"
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+ DIR="$(dirname "$(readlinkf "$0")")"
+ APP="${DIR%.app/Contents/*}".app
+ if [ "${APP}" = "${APP%.app}" ]; then
+ echo "Could not find Jalview.app" >&2
+ exit 2
+ fi
+ APPDIR="${APP}/Contents/Resources/app"
+ JAVA="${APPDIR}/jre/Contents/Home/bin/java"
+ JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
+else
+# NOT MACOS
+ DIR="$(dirname "$(readlink -f "$0")")"
+ APPDIR="${DIR}"
+ JAVA="${APPDIR}/jre/bin/java"
+fi
+
+SYSJAVA=java
GETDOWNTXT="${APPDIR}/getdown.txt"
-if [ -e "$GETDOWNTXT" ]; then
- CLASSPATH=""
- for x in $(grep -e 'code = ' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
- [ -n "$CLASSPATH" ] && CLASSPATH="${CLASSPATH}:"
- CLASSPATH="${CLASSPATH}${APPDIR}/${x}"
+
+CLASSPATH=""
+# save an array of JAR paths in case we're in WSL (see later)
+declare -a JARPATHS=()
+if [ -e "${GETDOWNTXT}" ]; then
+ # always check grep and sed regexes on macos -- they're not the same
+ for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
+ [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
+ CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
+ JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
done
else
echo "Cannot find getdown.txt" >&2
- exit 1
+ exit 3
+fi
+
+# WINDOWS ONLY (Cygwin or WSL)
+# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
+ if [ "$(uname -o)" = "Cygwin" ]; then
+ # CYGWIN
+ echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
+ CLASSPATH=$(cygpath -pw "${CLASSPATH}")
+ # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ elif uname -r | grep Microsoft >/dev/null; then
+ # WSL
+ echo "When using relative paths in args within WSL, please start with './' or '../'" >&2
+ CLASSPATH=""
+ for JARPATH in "${JARPATHS[@]}"; do
+ [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
+ CLASSPATH="${CLASSPATH}$(wslpath -aw "${JARPATH}")"
+ done
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ # annoyingly wslpath does not work if the file doesn't exist!
+ ARGBASENAME="$(basename "${ARG}")"
+ ARGDIRNAME="$(dirname "${ARG}")"
+ ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ JAVA="${JAVA}.exe"
+ SYSJAVA="java.exe"
+ fi
+fi
+
+# Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
+if [ \! -e "${JAVA}" ]; then
+ JAVA=$SYSJAVA
+ echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
+fi
+
+# check to see if $1 is set and is not start of other cli args
+OPEN=""
+if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
+ # first argument exists and does not start with a "-" and is not "open"
+ OPEN="-open"
fi
-"$JAVA" -cp "$CLASSPATH" jalview.bin.Launcher $OPEN "$@"
+# don't quote $OPEN (don't want it accidentally mistaken as an empty string arg!)
+"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"
git://source.jalview.org / jalview.git / blobdiff