install

#!/bin/bash
###################################################################################
##                                                                               ##
##  This script updates user profile to                                          ##
##    include the key variables $BLJ and $BLJ_PROJ                               ##
##    include the $BLJ/script dir in the $PATH                                   ##
##                                                                               ##
##  By default, the script determines the user's profile.                        ##
##  Optionally, supply the profile to use as an argument.                        ##
##  ex: ./install ~/.bashrc                                                      ##
##                                                                               ##
###################################################################################
BLJ="$( cd "$( dirname ${BASH_SOURCE[0]} )" && pwd )"

# If an arg is given, assume this is the user-profile that user has selected
# otherwise, determine the user_profile
user_profile=$1
if [ ${#user_profile} -eq 0 ]; then
	# Look for a default profile in the $USER $HOME dir
	get_default_profile() {
		if [ ${SHELL} == "/bin/bash" ]; then
			user_profile="${HOME}"/.bash_profile
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.bashrc
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.profile
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.bash_login
		elif [ ${SHELL} == "/bin/zsh" ]; then
			user_profile="${HOME}"/.zshrc
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.zshenv
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.zprofile
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.profile
			[ ! -f "${user_profile}" ] && user_profile="${HOME}"/.zlogin
		fi
		[ -f "${user_profile}" ] && echo "${user_profile}"
	}
	user_profile=$(get_default_profile)
	if [ ${#user_profile} -eq 0 ]; then
		echo "Could not determine user profile. Please supply one, example:"
		echo "./install ~/.bashrc"
		exit 1
	fi
fi

echo "Appending lines to user profile: $user_profile"

# If the profile already exists, back it up.
if [ ! -f "$user_profile" ]; then
	printf '%s\n' '#BioLockJ generated profile' > $user_profile
	echo "    Created profile: $user_profile"
elif [ ! -x "$user_profile" ]; then
	cp $user_profile $user_profile~
	echo "    Saved backup:  $user_profile~"
fi

echo "" >> $user_profile
echo "# installing BioLockJ" >> $user_profile

echo 'export BLJ='"$BLJ" >> $user_profile
echo "    Setting BLJ=$BLJ"

if [ ${#BLJ_PROJ} -gt 0 ] && [ -d ${BLJ_PROJ} ]; then
	echo '    Found existing $BLJ_PROJ: '"$BLJ_PROJ"
	echo "export BLJ_PROJ=$BLJ_PROJ" >> $user_profile
else
	echo '    Setting default BLJ_PROJ=$BLJ/pipelines'
	echo 'export BLJ_PROJ=$BLJ/pipelines' >> $user_profile
fi

echo 'export PATH=$BLJ/script:$PATH' >> $user_profile
echo "alias cd-blj='"'cd $(last-pipeline); quick_pipeline_view'"'" >> $user_profile
# should appear in the profile as:
# alias cd-blj='cd $(last-pipeline); quick_pipeline_view'

echo ""

export BLJ
export BLJ_PROJ=$BLJ/pipelines

VER=$(. $user_profile &>/dev/null ; biolockj --version 2>/dev/null )
if [ $? -eq 0 ] && [ ${#VER} -gt 0 ] ; then
	echo "Successfully installed BioLockJ version $VER"
	echo ""
	echo 'Start a new session and run "biolockj --help" to see options.'
else
	echo "Installation process complete."
	echo 'To verify installation, open a new session and type "biolockj --help"'
fi

echo ""
echo 'Then run a small pipeline:'
echo '"biolockj $BLJ/templates/myFirstPipeline/myFirstPipeline.properties" '
echo ""