--- /dev/null
+#!/usr/bin/env bash
+
+###############################
+# Wrapper for Jalview
+#
+# 2023-08-16 Jalview 2.11.3.0 has new command line arguments
+# Old command line arguments are currently detected and actioned
+# but are no longer supported and will be removed at a later date.
+#
+# See
+# Jalview -> Help -> Documentation -> Command Line -> introduction and reference
+# or
+# https://www.jalview.org/help/html/features/clarguments.html
+# for details of the new command line arguments.
+#
+# Note, in order to run commandline-only calls use
+# --headless
+#
+# By default, this wrapper executes java -version to determine the JRE version
+# Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to skip the version check.
+#
+# By default, this wrapper does NOT restrict the memory consumption of Jalview.
+# Set eg. JALVIEW_MAXMEM=1g to set the maximal memory of Jalview's VM
+#
+# This script is maintained in the Jalview repository in utils/conda/jalview.sh
+###############################
+
+declare -a ARGS=("${@}")
+ARG1=$1
+
+# this function is because there's no readlink -f in Darwin/macOS
+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 [ "$( uname -s )" = "Darwin" ]; then
+ ISMACOS=1
+fi
+
+# check for headless mode
+HEADLESS=0
+GUI=0
+HELP=0
+DEBUG=0
+for RAWARG in "${@}"; do
+ ARG="${RAWARG%%=*}"
+ case "${ARG}" in
+ --headless|--output|--image|--structureimage)
+ HEADLESS=1
+ ;;
+ --help|--help-*|--version)
+ HELP=1
+ ;;
+ --gui)
+ GUI=1
+ ;;
+ --debug)
+ DEBUG=1
+ ;;
+ esac
+
+ if [ "${HELP}" = 1 ]; then
+ # --help takes precedence
+ HEADLESS=1
+ GUI=0
+ elif [ "${GUI}" = 1 ]; then
+ # --gui takes precedence over --headless
+ HEADLESS=0
+ fi
+done
+
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+ DIR="$(dirname "$(readlinkf "$0")")"
+ JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${DIR}/jalview_logo.png" )
+else
+# NOT MACOS
+ DIR="$(dirname "$(readlink -f "$0")")"
+fi
+
+if [ "${HEADLESS}" = 1 ]; then
+ # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes
+ JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+fi
+
+JAVA=java
+
+# decide which jalview jar to launch - either 'j11' or 'j1.8'
+if [[ "$JALVIEW_JRE" != "j11" && "$JALVIEW_JRE" != "j1.8" ]]; then
+ JALVIEW_JRE="j11"
+ # if java 8 is installed we pick the j1.8 build
+ if [[ $( "${JAVA}" -version 2>&1 | grep '"1.8' ) != "" ]]; then
+ JALVIEW_JRE="j1.8"
+ fi
+fi
+
+JARPATH="${DIR}/jalview-all-${JALVIEW_JRE}.jar"
+
+# check if memory maximum is set and if so forward to java-based jalview call
+if [ \! -z "$JALVIEW_MAXMEM" ]; then
+ JVMARGS=( "${JVMARGS[@]}" "-Xmx${JALVIEW_MAXMEM}" )
+fi
+
+# WINDOWS ONLY (Cygwin or WSL)
+# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
+ if [ "$(uname -o)" = "Cygwin" ]; then
+ # CYGWIN
+ JARPATH="$(cygpath -pw "${JARPATH}")"
+ # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
+ ARGS=()
+ for ARG in "${@}"; do
+ if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+ ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
+ else
+ ARGS=( "${ARGS[@]}" "${ARG}" )
+ fi
+ done
+ elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+ # WSL
+ JARPATH="$(wslpath -aw "${JARPATH}")"
+ ARGS=()
+ for ARG in "${@}"; 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="${JAVA}.exe"
+ fi
+fi
+
+# get console width -- three ways to try, just in case
+if command -v tput 2>&1 >/dev/null; then
+ COLUMNS=$(tput cols) 2>/dev/null
+elif command -v stty 2>&1 >/dev/null; then
+ COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
+elif command -v resize 2>&1 >/dev/null; then
+ COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
+fi
+JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" "${ARGS[@]}"
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}"
git://source.jalview.org / jalview.git / blobdiff