# Commands and environment variables for local additions
# to BIRCH

if ( $BIRCH_DEBUG == 1 ) echo Running local.cshrc.source

# VALUES SET HERE OVERRIDE SETTINGS IN cshrc.source

# $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.
#
setenv BIRCH_LOGGING 1

#-------------------------- Platform-dependent variables

# BIRCHJAVACMD - Java command for running birchconfig and seahawk



# ----------------------------------------------------------------------
# force prompt to display durrent working directory
#    set prompt="{`hostname`:$cwd}"
#    alias cd            'cd \!*; set prompt="{`hostname`:$cwd"}'
#    alias popd          'popd \!*; set prompt="{`hostname`:$cwd"}'
#   alias pushd         'pushd \!*; set prompt="{`hostname`:$cwd"}'
# ----------------------------------------------------------------------

# ----------------------------------------------------------------------
# force prompt to display durrent working directory
    set prompt="{$HOSTNAME":"$cwd"}
    alias cd            'cd \!*; set prompt="{$HOSTNAME":"$cwd"}'
    alias popd          'popd \!*; set prompt="{$HOSTNAME":"$cwd"}'
    alias pushd         'pushd \!*; set prompt="{$HOSTNAME":"$cwd"}'
# ----------------------------------------------------------------------

#-------------------------- MBCRR
setenv MBCRR   $BIRCH/local/pkg/MBCRR-Package
setenv mbcrr   $MBCRR
setenv PLSEARCH_HOME  $MBCRR/plsearch-4.2
# -----------------------------PIMA 
setenv PIMA_HOME $birch/local/dat/pima

#--------------------------- R eg. BioConductor
if (-z "$R_LIBS") then
    setenv R_LIBS $BIRCH/R/x86_64-redhat-linux-gnu-library/3.4
else
    setenv R_LIBS ${R_LIBS}:$BIRCH/R/x86_64-redhat-linux-gnu-library/3.4
endif

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

#-------------------------- VISA
setenv HELPPATH $doc/visa

#--------------------------- XLANDSCAPE
setenv XENVIRONMENT $BIRCH/local/dat/XLandscape/XLand

#-------------------------- DNA-GUI
#No longer works on Solaris
#setenv XAPPLRESDIR $BIRCH/XAPPLRESDIR

#------------------------ 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!
setenv BIRCH_TMP /usr/local/tmp