X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=utils%2Fconda%2Fjalview.sh;fp=utils%2Fconda%2Fjalview.sh;h=9ac28075bc3ce1c9c0b15a0a69a61f0a2b8b9aa2;hb=e83ce5d8ef826fc0b509a51f154abdf734501077;hp=0000000000000000000000000000000000000000;hpb=786475501a15799d7c4058dbf74e4bf896d03736;p=jalview.git

diff --git a/utils/conda/jalview.sh b/utils/conda/jalview.sh
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+#!/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=("${@}")
+
+# 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|-h)
+      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 "$0")")"
+  if [ -e "${DIR}/jalview_logo.png" ]; then
+    JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${DIR}/jalview_logo.png" )
+  fi
+else
+# NOT MACOS
+  DIR="$(dirname "$(readlink -f "$0")")"
+fi
+
+if [ "${HEADLESS}" = 1 ]; then
+  # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
+  if [ "${HELP}" = 1 ]; then
+    JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+  fi
+  # this suppresses the Java icon appearing in the macOS Dock
+  if [ "${ISMACOS}" = 1 ]; then
+    JVMARGS=( "${JVMARGS[@]}" "-Dapple.awt.UIElement=true" )
+  fi
+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}" )
+
+function quotearray() {
+  QUOTEDVALS=""
+  for VAL in "${@}"; do
+    if [ \! "$QUOTEDVALS" = "" ]; then
+      QUOTEDVALS="${QUOTEDVALS} "
+    fi
+    QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
+  done
+  echo $QUOTEDVALS
+}
+
+JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
+ARGSSTR=$(quotearray "${ARGS[@]}")
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -jar \""${JARPATH}"\" ${ARGSSTR}
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}"