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dockstore
executable file
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dockstore
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#!/usr/bin/env bash
set -o errexit
# Ensure this file is executable via `chmod a+x dockstore`, then place it
# somewhere on your $PATH, like ~/bin. The rest of SeqWare will be
# installed upon first run into the ~/.dockstore directory.
# Encase variables inside brackets to prevent issues.
# $DOCKSTORE_VERSION would cause problems if $DOCKSTORE exists. ${DOCKSTORE_VERSION} would be better.
DEFAULT_DOCKSTORE_VERSION="1.4.0-alpha.5"
export DOCKSTORE_VERSION="${DOCKSTORE_VERSION:-"$DEFAULT_DOCKSTORE_VERSION"}"
case ${DOCKSTORE_VERSION} in
*SNAPSHOT) SNAPSHOT="YES" ;;
*) SNAPSHOT="NO" ;;
esac
if [[ "$OSTYPE" == "cygwin" ]] || [[ "$OSTYPE" == "msys" ]]; then
delimiter=";"
else
delimiter=":"
fi
if [[ "$OSTYPE" == "cygwin" ]]; then
cygwin=true
else
cygwin=false
fi
if [ `id -u` -eq 0 ] && [ "$DOCKSTORE_ROOT" = "" ]; then
echo "WARNING: You're currently running as root; probably by accident."
echo "Press control-C to abort or Enter to continue as root."
echo "Set DOCKSTORE_ROOT to disable this warning."
read _
fi
export DOCKSTORE_HOME="${DOCKSTORE_HOME:-"$HOME/.dockstore"}"
# export DOCKSTORE_HOME="${DOCKSTORE_HOME:-"$HOME/dockstore"}"
if ${cygwin}; then
export DOCKSTORE_HOME=`cygpath -w "$DOCKSTORE_HOME"`
fi
export DOCKSTORE_JAR="$DOCKSTORE_HOME/self-installs/dockstore-client-$DOCKSTORE_VERSION.jar"
export DOCKSTORE_SETTINGS="${DOCKSTORE_SETTINGS:-"$DOCKSTORE_HOME/config"}"
# normalize $0 on certain BSDs
if [ "$(dirname "$0")" = "." ]; then
if ! SCRIPT="$(which $(basename "$0"))"; then
if [[ "$@" != *"--script"* ]]; then
(>&2 echo "dockstore needs to be on PATH for certain commands to work (like --upgrade)")
fi
fi
else
SCRIPT="$0"
fi
# resolve symlinks to the script itself portably
while [ -h "$SCRIPT" ] ; do
ls=`ls -ld "$SCRIPT"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
SCRIPT="$link"
else
SCRIPT="$(dirname "$SCRIPT"$)/$link"
fi
done
function make_native_path {
# ensure we have native paths
if ${cygwin} && [[ "$1" == /* ]]; then
echo -n "$(cygpath -wp "$1")"
elif [[ "$OSTYPE" == "msys" && "$1" == /* ]]; then
echo -n "$(sh -c "(cd $1 2</dev/null && pwd -W) || echo $1 | sed 's/^\\/\([a-z]\)/\\1:/g'")"
else
echo -n "$1"
fi
}
# usage : add_path PATH_VAR [PATH]...
function add_path {
local path_var="$1"
shift
while [ -n "$1" ];do
# http://bashify.com/?Useful_Techniques:Indirect_Variables:Indirect_Assignment
export ${path_var}="${!path_var}${delimiter}$(make_native_path "$1")"
shift
done
}
add_path CLASSPATH "$DOCKSTORE_JAR"
BOOTCLASSPATH="-Xbootclasspath/a:$DOCKSTORE_JAR"
if [ ! -r "$DOCKSTORE_JAR" -a "$1" != "self-install" -a "$1" != "self-check-install" -a "$1" != "init" ]; then
"$0" self-install
if [ $? != 0 ]; then
exit $?
fi
fi
if [ ! -r "$DOCKSTORE_SETTINGS" -a "$1" != "self-install" -a "$1" != "self-check-install" -a "$1" != "init" ]; then
"$0" init
exit $?
fi
if [ "$HTTP_CLIENT" = "" ]; then
if type -p curl >/dev/null 2>&1; then
if [ "$https_proxy" != "" ]; then
CURL_PROXY="-x $https_proxy"
fi
HTTP_CLIENT="curl --retry 20 $CURL_PROXY -f -L -o"
else
HTTP_CLIENT="wget -O"
fi
fi
# TODO: explain what to do when Java is missing
export JAVA_CMD="${JAVA_CMD:-"java"}"
# Support $JAVA_OPTS for backwards-compatibility.
export JVM_OPTS="${JVM_OPTS:-"$JAVA_OPTS"}"
# Handle jline issue with cygwin not propagating OSTYPE through java subprocesses: https://github.com/jline/jline2/issues/62
cygterm=false
if ${cygwin}; then
case "$TERM" in
rxvt* | xterm* | vt*) cygterm=true ;;
esac
fi
if ${cygterm}; then
JVM_OPTS="$JVM_OPTS -Djline.terminal=jline.UnixTerminal"
stty -icanon min 1 -echo > /dev/null 2>&1
fi
function download_failed_message {
echo "Failed to download $1"
echo "It's possible your HTTP client's certificate store does not have the"
echo "correct certificate authority needed. This is often caused by an"
echo "out-of-date version of libssl. Either upgrade it or set HTTP_CLIENT"
echo "to turn off certificate checks:"
echo " export HTTP_CLIENT=\"wget --no-check-certificate -O\" # or"
echo " export HTTP_CLIENT=\"curl --insecure -f -L -o\""
echo "It's also possible that you're behind a firewall haven't yet"
echo "set HTTP_PROXY and HTTPS_PROXY."
}
if [ "$1" = "self-install" ]; then
if [ -r "$DOCKSTORE_JAR" ]; then
echo "The self-install jar already exists at $DOCKSTORE_JAR."
echo "If you wish to re-download, delete it and rerun \"$0 self-install\"."
exit 1
fi
(>&2 echo "Downloading Dockstore to $DOCKSTORE_JAR now...")
mkdir -p "$(dirname "$DOCKSTORE_JAR")"
if [ ${SNAPSHOT} = "YES" ]; then
DOCKSTORE_URL="file:///$HOME/.m2/repository/io/dockstore/dockstore-client/$DOCKSTORE_VERSION/dockstore-client-$DOCKSTORE_VERSION-shaded.jar"
elif [ -r "/$HOME/.m2/repository/io/dockstore/dockstore-client/$DOCKSTORE_VERSION/dockstore-client-$DOCKSTORE_VERSION-shaded.jar" ]; then
# for testing, if you have a local release version, just use it
DOCKSTORE_URL="file:///$HOME/.m2/repository/io/dockstore/dockstore-client/$DOCKSTORE_VERSION/dockstore-client-$DOCKSTORE_VERSION-shaded.jar"
else
# DOCKSTORE_URL="https://artifacts.oicr.on.ca/artifactory/collab-release/io/dockstore/dockstore-client/$DOCKSTORE_VERSION/dockstore-client-$DOCKSTORE_VERSION-shaded.jar"
DOCKSTORE_URL="https://github.com/ga4gh/dockstore/releases/download/$DOCKSTORE_VERSION/dockstore-client-$DOCKSTORE_VERSION-shaded.jar"
fi
(>&2 echo "$DOCKSTORE_URL")
${HTTP_CLIENT} "$DOCKSTORE_JAR.pending" "$DOCKSTORE_URL"
if [ $? == 0 ]; then
# TODO: checksum
mv -f "$DOCKSTORE_JAR.pending" "$DOCKSTORE_JAR"
else
rm "$DOCKSTORE_JAR.pending" 2> /dev/null
download_failed_message "$DOCKSTORE_URL"
exit 1
fi
elif [ "$1" = "init" ]; then
if [ -r "$DOCKSTORE_SETTINGS" ]; then
echo "The Dockstore settings file already exists at $DOCKSTORE_SETTINGS."
echo "If you wish to re-initialize, delete it and rerun \"$0 init\"."
exit 1
fi
echo "DOCKSTORE COMMAND LINE"
echo "----------------------"
echo "Welcome to the command line tool for the Dockstore. This bootstrap process will"
echo "ask you a few questions, download, and configure the command line tool."
echo
echo
echo "Have you setup an account at http://www.dockstore.org/?"
echo -n "Y/N> "
read HASACCOUNT
if [ "$HASACCOUNT" = "Y" ] || [ "$HASACCOUNT" = "y" ]; then
mkdir -p "$(dirname "$DOCKSTORE_SETTINGS")"
touch ${DOCKSTORE_SETTINGS}
chmod 600 ${DOCKSTORE_SETTINGS}
echo
echo "What is your token?"
read TOKEN
echo "token: $TOKEN" >> ${DOCKSTORE_SETTINGS}
echo "What is your server-url?"
read SERVER_URL
echo "server-url: $SERVER_URL" >> ${DOCKSTORE_SETTINGS}
echo
echo "Created Dockstore settings file at $DOCKSTORE_SETTINGS"
echo
echo "Downloading default file-provisioning plugins"
${JAVA_CMD} ${DOCKSTORE_JVM_OPTS} io.dockstore.client.cli.Client plugin download
echo "Dockstore is ready to use!"
else
echo "Please setup an account at http://www.dockstore.org/"
fi
else
# from https://stackoverflow.com/questions/7334754/correct-way-to-check-java-version-from-bash-script
if type -p java > /dev/null; then
_java=java
else
echo "Java was not installed or is not on your PATH."
exit -100;
fi
if [[ "$_java" ]]; then
version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
if [[ "$version" < "1.8" ]]; then
echo "Dockstore requires Java version 1.8 and above."
exit -100;
fi
fi
${JAVA_CMD} ${DOCKSTORE_JVM_OPTS} io.dockstore.client.cli.Client "$@"
EXIT_CODE=$?
if ${cygterm} ; then
stty icanon echo > /dev/null 2>&1
fi
exit $EXIT_CODE
fi