labkeyDocker/bin/installLabkey.sh

#!/bin/bash
#binaries available at labkey-public/Resources
#and
#https://www.labkey.org/Documentation/list-grid.view?listId=634&query.ignoreFilter=1
#recent ones, here
#https://www.labkey.org/Documentation/wiki-page.view?name=prevReleases

. $(dirname $0)/env.sh

LABKEY=LabKey22.3.2-3-community

if [ $# -gt 0 ] ; 
then
	case $1 in
	18.1)
		LABKEY=LabKey18.1-57017.17-professional-bin;;
	18|18.3)
		LABKEY=LabKey18.3.3-62784.7-community-bin;;
   19|19.3)
		LABKEY=LabKey19.3.10-65330.20-community-bin;;
	20|20.11)
		LABKEY=LabKey20.11.8-10-community;;
	21|21.11)
		LABKEY=LabKey21.11.11-14-community;;
	22|22.3)        
      LABKEY=LabKey22.3.2-3-community;;
   23|23.11)
      LABKEY=LabKey23.11.11-11-13-community;;
   *) 
      echo "Failed to find appropriate version for $1"
      exit 1;
	esac;

fi;

TARGET=${LABKEY_DIR}
if [ $# -gt 1 ] ; 
then
   TARGET=$2;
fi;

echo "Using $LABKEY; setting up in $TARGET";

#full path to source
SFW_SRC=$HOME/packages/$LABKEY.tar.gz

#this is temp only
TMP_DIR=$HOME/tmp

if [ ! -d ${TMP_DIR} ] ; 
then
	mkdir ${TMP_DIR};
fi;

#target LabkeyDir
#is there anything relevant in $TARGET?
if [ ! -d $TARGET ] ; 
then
	mkdir $TARGET;
fi;

#unpack to ${TMP_DIR}/$LABKEY
TMP_LABKEY=${TMP_DIR}/$LABKEY;

#make sure we are starting from a clean slate
if [ -d ${TMP_LABKEY} ] ; then
   rm -rf ${TMP_LABKEY};
fi;

#untar in ${TMP_DIR}
cd ${TMP_DIR} && tar xvzf ${SFW_SRC};
echo "Using distribution in ${TMP_LABKEY}";

#copy from $TMP_LABKEY to labkey space in docker
LABKEY_SRC_DIRS=("labkeywebapp" "modules" "pipeline-lib")

for d in ${LABKEY_SRC_DIRS[@]} ; 
do
   mv ${TMP_LABKEY}/$d $TARGET/$d;
done;

#check if required dirs are missing and create them
LABKEY_DIRS=("files" "externalModules")

for d in ${LABKEY_DIRS[@]} ; 
do
   if [ ! -d $TARGET/$d ] ; then
      mkdir $TARGET/$d;
   fi;
done;

#tomcat-lib goes to tomcat user space in docker
mv ${TMP_LABKEY}/tomcat-lib ${TOMCAT_DIR}/lib

echo "Cleanup of tem directory";
rm -rf ${TMP_LABKEY}

echo "Done"
echo "Change COMPOSE to appropriate yaml in bin/env.sh!"