# Commands and environment variables for local additions
# to BIRCH

if [ $BIRCH_DEBUG -eq 1 ]  
   then
      echo Running $BIRCH/local/admin/local.profile.source  
fi

# applies colors to particular file types in ls output
alias ls="ls --color"

# $BIRCH_LOGGING=1 means that when users log in a message will
# be appended to local/admin/logins.log, and when gde is launched,
# a message is appended to local/admin/gde.log
#
# DO NOT use this option if the BIRCH filesystem is mounted
# read-only for users.
#
BIRCH_LOGGING=0
export BIRCH_LOGGING

# Location of specific versions of Java
# Depending on the program, you need to specify either which
# directory has Java (JAVAx_HOME), or the full path to the java command (JAVAx_CMD).
# Some examples are given below. 
# You can list all versions of Java that are installed on your system by
# typeing 'findjava.sh'.
#JAVA8_HOME="/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-1.el7_9.x86_64/jre"
#JAVA8_CMD="/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-1.el7_9.x86_64/jre/bin/java"
#export JAVA11_HOME="/usr/lib/jvm/java-11-openjdk-11.0.15.0.9-2.el7_9.x86_64"
export JAVA11_HOME="/usr/lib/jvm/java-11"
export JAVA11_CMD="$JAVA11_HOME/bin/java"
export JAVA17_HOME="/usr/lib/jvm/java-17"
export JAVA17_CMD="$JAVA17_HOME/bin/java"

#-------------------------- EMBOSS
COUNT=`echo $PATH | grep -c EMBOSS`
if [ "$COUNT" -eq "0" ]
   then
   case "$BIRCH_PLATFORM" in
     solaris-sparc)
       PLPLOT_LIB=$BIRCH/local/pkg/EMBOSS/solaris-sparc/lib
       PATH=$PATH\:$BIRCH/local/pkg/EMBOSS/solaris-sparc/bin    
       ;;
     solaris-amd64)
       PLPLOT_LIB=$BIRCH/local/pkg/EMBOSS/solaris-amd64/lib
       PATH=$PATH\:$BIRCH/local/pkg/EMBOSS/solaris-amd64/bin   
       ;;
     linux-intel)
       PLPLOT_LIB=$BIRCH/local/pkg/EMBOSS/linux-intel/lib
       PATH=$PATH\:$BIRCH/local/pkg/EMBOSS/linux-intel/bin    
       ;;
     linux-x86_64)
       PLPLOT_LIB=$BIRCH/local/pkg/EMBOSS/linux-x86_64/lib
       PATH=$PATH\:$BIRCH/local/pkg/EMBOSS/linux-x86_64/bin    
       ;;    
     *)  
       PLPLOT_LIB=$BIRCH/local/pkg/EMBOSS/solaris-sparc/lib
       PATH=$PATH\:$BIRCH/local/pkg/EMBOSS/solaris-sparc/bin  
       ;;
   esac
   export PATH PLPLOT_LIB
fi


#-------------------------- MBCRR
MBCRR=$BIRCH/MBCRR-Package
mbcrr=$MBCRR
PLSEARCH_HOME=$MBCRR/plsearch-4.2
export MBCRR mbcrr PLSEARCH_HOME

# --------------------------- PIMA
PIMA_HOME=$BIRCH/local/dat/pima
export PIMA_HOME

#--------------------------- R eg. BioConductor

if [ -z ${R_LIBS} ] 
then
    R_LIBS=$BIRCH/R/x86_64-redhat-linux-gnu-library/3.4
else
    R_LIBS=${R_LIBS}:$BIRCH/R/x86_64-redhat-linux-gnu-library/3.4
fi
export R_LIBS

#--------------------------- TIGR TM4
# If your system has enough memory, set this to at least 512 or 1024
TMEV_JAVA_MEMORY=1024
export TMEV_JAVA_MEMORY

#-------------------------- VISA
HELPPATH=$doc/visa
export HELPPATH

#--------------------------- XLANDSCAPE
XENVIRONMENT=$BIRCH/local/dat/XLandscape/XLand
export XENVIRONMENT

#------------------------ TEMPORARY DIRECTORIES --------------
# This variable may be changed to a directory where
# temporary files may be written for some
# scripts which run programs that generate very large
# temporary files. Do NOT use /tmp. If that directory
# gets too full, it can seriously impede the entire system!
BIRCH_TMP=/usr/local/tmp
export BIRCH_TMP