#! /bin/sh
# [The above is just for emacs -- this file should not be executed.]

# CCP4 setup file for bash or ksh (untested) users.  Actually, the aliases 
# can't work asis in ksh.  Should use builtins instead and not worry about
# ease of keeping in step with the csh one.

# $Id: ccp4.setup-sh,v 1.68 2012/07/04 09:20:49 ccb Exp $

# This file is site specific and may also contain machine-specifics.  The CCP4
# administrator will have to edit this file and then have anyone who wants to
# use CCP4 source it from their .login file.  They will require the full path
# name since no environment variables relevant to CCP4 are known until this is
# executed.

# For sites with more than one machine, it is recommended that the suite is
# installed on a single machine and other machines access the source code, and
# shareable files (such as this one) via shared file systems with NFS, RFS
# etc.  Non-shareable files reside in $CBIN and $CLIB (see below).

# Copy this file to ccp4.setup and customise it for your needs. There are
# three sections. You MUST check the first section. You may want to check
# the second. You don't need to look at the third.

################### THIS SECTION MUST BE EDITED #####################

# CCP4_MASTER is the location of the top-level directory containing `ccp4'.  
# This is assumed to be shared between machines at a multi-machine site.

export CCP4_MASTER=/xtal
export CCP4=$CCP4_MASTER/ccp4-6.3.0

# CCP4_SCR: a per-user directory for run-time-generated scratch
# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
# BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR

export CCP4_SCR=/tmp/$USER	
# check to see if this exists and if not try to make it
test -d $CCP4_SCR || mkdir $CCP4_SCR
test -d $CCP4_SCR || echo "Unable to assign CCP4_SCR. This will cause probs."

export BINSORT_SCR=$CCP4_SCR

### CCP4i setup - you may need to edit CCP4I_TCLTK ###
# CCP4I_TOP - the top directory of the interface
export CCP4I_TOP=$CCP4/share/ccp4i
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
#               as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
#               For 'standard' installations this is /usr/local/bin
#               but note the SGI distributed version of Tcl/Tk is not 
#               appropriate version
export CCP4I_TCLTK=/usr/bin
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
export CCP4I_HELP=$CCP4I_TOP/help


###Optional - setting http_proxy environment
#The commented out 'export' line below may have to be declared to download
#and edit protein sequences using the new "Import/Edit protein sequences"
#task. If so, uncomment this line and replace example proxy URL with your 
#relevant URL

#export HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah

################### NOVICE USERS STOP HERE #####################

################### OPTIONS TO CUSTOMISE CCP4 #####################

# Set GFORTRAN_UNBUFFERED_ALL to either 1 or Y to ensure that the logfile
# output from programs compiled with Gfortran is in the correct order.
# Note that there will be some performance penalty for this.
#export GFORTRAN_UNBUFFERED_ALL=Y

# Gfortran 4.3.0 has new GFORTRAN_UNBUFFERED_PRECONNECTED variable
# to make only STDOUT and STDERR unbuffered.
# Unlike GFORTRAN_UNBUFFERED_ALL it doesn't slow down notably refmac
# and probably also other programs.
# Details: http://gcc.gnu.org/bugzilla/show_bug.cgi?id=33795
export GFORTRAN_UNBUFFERED_PRECONNECTED=Y

# By default, CCP4 directories are appended to the end of paths (PATH,
# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
# to 1, then they will be prepended to the beginning of paths.
# When deciding local policy, bear in mind the possible existence of
# other CCP4 installations, and the possibility of non-CCP4 programs
# with conflicting names.
ccp4_first_in_path=1

# The following checks the CCP4 server for available updates, and reports back.
# Uncomment this line if you want to know about available updates.

#eval python -V >& /dev/null 2>&1 && python $CCP4/etc/ccp4_updates.py -l

# The commented-out switch statement below provides an example of how
# to use this file for several machines/architectures sharing $CCP4_MASTER.
# If necessary, uncomment and edit this.  Otherwise, if you're only supporting
# a single system alter the uncommented part as necessary.
#
# The significance of the environment variables is as follows:
#   CBIN: location of the executables -- must be on your path (see below);
#   CLIB: location of (binary) library files such as libccp4.a and libccp4.so;
#   MANPATH: set this if your system's `man' looks at such an environment
#      variable to determine where to look for man pages.  By adding 
#      $CCP4/man to the normal path you get the CCP4 man pages 
#      with keyword searching as system ones.  
#   MCTYPE: used for LAUE make -- see LAUE documentation
#   CCP4_BROWSER: set this if you intend to use the html documentation
#      (recommended).  It should have the path and name of a html browser eg
#      /usr/bin/X11/mozilla or /usr/local/bin/lynx. The browser will be
#      started with the alias ccp4help and will open the file
#      $CHTML/INDEX.html.

#   case `hostname` in			# edit this case statement if used
#                                       # for multiple systems
#   foo)
    export CBIN=$CCP4/bin		
    export CLIB=$CCP4/lib	

    export CCP4_BROWSER=firefox             
    export MANPATH=$CCP4/man:$MANPATH           # edit this if necessary
    if test -d $CCP4_MASTER/laue
    then
      export MCTYPE=unix 			# (only for Laue)
    fi
#     ;;
#   *)
#     echo "CCP4 not implemented on this system"
#     exit 1
#     ;;
# esac

# The following are for all systems

export CCP4_LIB=$CLIB
export CCP4_BIN=$CBIN

# CLASSPATH for Java
export CLASSPATH=$CBIN:$CLASSPATH                      # edit this if necessary

### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
export PLOT_COMMAND='lp -s'  
export PRINT_COMMAND='lp -s'    

# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
export HARVESTHOME=$HOME     

### CCP4_OPEN ###
# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened 
# as NEW that already exist.  Novices should use 'NEW' to avoid inadvertant 
# over-writing of existing files, which is then treated as a fatal error.

export CCP4_OPEN=UNKNOWN	

### BINSORT_MEM ###
# BINSORT_MEM is workspace used by the binsort program.  In principle this
# value is machine-dependent.  It may benefit from being enlarged, but values
# higher than 2M have been reported to cause excessive paging on some systems.
# You might like to experiment with a program such as fft with different
# values -- 102400 (bytes) is the default.  csh's `time' command can tell you
# about paging.
#
#  export BINSORT_MEM=8388608

# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so)
# at runtime
if test "$LD_LIBRARY_PATH"; then
  if test $ccp4_first_in_path -eq 1; then
    export LD_LIBRARY_PATH=$CLIB:$LD_LIBRARY_PATH
  else
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CLIB
  fi
else
  export LD_LIBRARY_PATH=$CLIB
fi

# DYLD_LIBRARY_PATH specifies where to find dynamic libraries
# (e.g. libccp4.dylib) at runtime
if test "$DYLD_LIBRARY_PATH"; then
  if test $ccp4_first_in_path -eq 1; then
    export DYLD_LIBRARY_PATH=$CLIB:$DYLD_LIBRARY_PATH
  else
    export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$CLIB
  fi
else
  export DYLD_LIBRARY_PATH=$CLIB
fi

### XAPPLRESDIR ###

# If you want to use xloggraph/xplot84driver, you need to get the application
# defaults picked up somehow.  As distributed, the file can't just live in an
# application defaults directory since it requires reading by xrdb to sort out
# the differences for monochrome displays.  At Daresbury a version of the file
# assuming a monochrome display is kept in the directory
# $CCP4_LIB/X11/app-defaults and this is picked up through the
# XUSERFILESEARCHPATH environment variable.  That means you only see black and
# white on a colour display.  Alternatively you might make sure that it is
# read by xrdb on startup of the X Windows system or delegate the
# responsibility to users to run it.  There are disadvantages to putting an
# invocation of xrdb in here, one being that the correct value of DISPLAY may
# not be set at the time this file is read.  Thus edit this part as
# appropriate.  (SunOS will normally want to use /usr/openwin or $OPENWINHOME
# instead of /usr; others may want /usr/local/lib or somw such):

# export XAPPLRESDIR=/sw/etc/app-defaults/

if test -d $CCP4_LIB/X11/app-defaults ; then
  if test "$XUSERFILESEARCHPATH"; then
    export XUSERFILESEARCHPATH=$CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH
  else
    export XUSERFILESEARCHPATH=$CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults
  fi
fi

### TRAPPFE ###
# TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on floating
# point exceptions under IRIX.  It shouldn't cause harm on other systems, but
# edit this to comment it out if necessary. Have now added a case statement.

case `uname` in
*IRIX* )
  export TRAP_FPE="OVERFL=ABORT; DIVZERO=ABORT; INVALID=ABORT"
  ;;
* )
  ;;
esac

# The following can be used to put a message of the day to announce news about
# CCP4 or whatever to CCP4 users.  You might also want to edit this part to
# have machine-specific messages dependent on `hostname`.
test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg

################### EXPERIENCED USERS STOP HERE #####################

#Python path for the subprocess fixed module

if test $ccp4_first_in_path -eq 1; then
    export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
else
    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
fi

################### THE REST SHOULDN'T NEED EDITING #####################

### dbCCP4i database handler setup ###

export DBCCP4I_TOP=${CCP4}/share/dbccp4i

### IMOSFLM environment is now defined here

export MOSFLM_EXEC=${CBIN}/ipmosflm
export MOSFLM_WISH=${CCP4I_TCLTK}/wish

### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
# so on multiple installs it need to be unique and not in $CLIBD

export MMCIFDIC=$CCP4/share/ccif/cif_mmdic.lib

### MOLREPLIB Point to the location of the files bs-zeros.dat  ps.resource  symlib.blc
# They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /

export MOLREPLIB=$CCP4/lib/data/monomers/

### CRANK points to location of Crank automation suite within ccp4i

export CRANK=$CCP4I_TOP/crank
export CCP4_CRANK=1

### XIA2 setup
# XIAROOT directory (default is under the share folder)

if test -e $CCP4/share/xia2/setup.sh
then
export XIA2_HOME=$CCP4/share/xia2
. $CCP4/share/xia2/setup.sh
fi

# Note: The PATH is updated with the xia2 Applications directory in the 
# construct below.

### PISA_CONF_FILE is the config file needed to run the stand-alone PISA,
#   though this can be set on the command line too.

if test -e $CCP4/share/pisa/pisa.cfg 
then
  export PISA_CONF_FILE=$CCP4/share/pisa/pisa.cfg
fi

### CLIBD_MON Point to the location of the dictionary files for REFMAC5
# They are distributed with CCP4 in $CLIBD/monomers. This env must have 
# the trailing \ or /

export CLIBD_MON=$CCP4/lib/data/monomers/

### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
# (essential for the relevant programs)
export PUBLIC_FONT84=$CLIB/data/ccp4/font84.dat  # plot84 fonts [used by plot84lib]

# location of VMS-style help files required for mosflm [used by hlplib, chelp,
#   chlp, (ip)mosflm]:
export CCP4_HELPDIR=$CCP4/help/            # NB trailing /

# Rasmol path. Needed for prog. to find rasmol.hlp
export RASMOLPATH=$CCP4/x-windows/RasMol

# CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
# on the path in an appropriate order for scripts to be used as wrappers for
# binaries of the same name.  Put ccp4 stuff after the current path to avoid
# confusion with `.' or whatever in the path:
#
# This construct prevents the path getting longer each time ccp4.setup is
# executed (A. Perrakis)
ccp4pathlist="${CCP4}/etc ${CBIN} ${CCP4I_TOP}/bin ${DBCCP4I_TOP}/bin"
#
for dir in ${ccp4pathlist}
do
  if [ `expr ":${PATH}:" : ".*:${dir}:"` -eq 0 ]; then
    if test $ccp4_first_in_path -eq 1; then
      PATH=${dir}:${PATH}
    else
      PATH=${PATH}:${dir}
    fi
  fi
done

# Optional (useful) additional environment variables
  export CCP4=$CCP4
  export CDOC=$CCP4/doc
  export CHTML=$CCP4/html
  export CETC=$CCP4/etc
  export CEXAM=$CCP4/examples
  export CINCL=$CCP4/include
  export CLIBD=$CCP4/lib/data
  export CLIBS=$CCP4/lib/libccp4
  export CPROG=$CCP4/src

# useful aliases, at least for developers
  alias ccp4='pushd $CCP4>/dev/null'
  alias xtal='pushd $CCP4_MASTER>/dev/null'
  alias cbin='pushd $CBIN>/dev/null'
  alias cetc='pushd $CETC>/dev/null'
  alias cprog='pushd $CPROG>/dev/null'
  alias cincl='pushd $CINCL>/dev/null'
  alias clib='pushd $CLIB>/dev/null'
  alias clibd='pushd $CLIBD>/dev/null'
  alias clibs='pushd $CLIBS>/dev/null'
  alias cbin='pushd $CBIN>/dev/null'
  alias cexam='pushd $CEXAM>/dev/null'
  alias cdoc='pushd $CDOC>/dev/null'
  alias chtml='pushd $CHTML>/dev/null'
  alias ccp4help='$CCP4_BROWSER $CHTML/INDEX.html'

### laue, lget, linkimages ###
### only if we have the Laue software suite...
  if ( test -d $CCP4_MASTER/laue ) ; then

# Essential aliases for the Laue software suite

    alias laue='$CCP4_MASTER/laue/cmd/laue.cmd'
    alias lget='$CCP4_MASTER/laue/cmd/lget.cmd'
    alias linkimages='$CCP4_MASTER/laue/cmd/linkimages.cmd'

# additional useful aliases for Laue directories
    alias llaue='pushd $CCP4_MASTER/laue'
    alias lsrc='pushd $CCP4_MASTER/laue/src>/dev/null'
    alias llib='pushd $CCP4_MASTER/laue/lib>/dev/null'
    alias llibs='pushd $CCP4_MASTER/laue/lib/src>/dev/null'
    alias ldoc='pushd $CCP4_MASTER/laue/doc>/dev/null'
    alias lmak='pushd $CCP4_MASTER/laue/make>/dev/null'
    alias lutils='pushd $CCP4_MASTER/laue/utils>/dev/null'
    alias lcmd='pushd $CCP4_MASTER/laue/cmd>/dev/null'
    alias ldl='pushd $CCP4_MASTER/laue/dl>/dev/null'
    alias ltestd='pushd $CCP4_MASTER/laue/testdata>/dev/null'
    alias lxdl='pushd $CCP4_MASTER/laue/xdl_view>/dev/null'
    alias lxdls='pushd $CCP4_MASTER/laue/xdl_view/src>/dev/null'
    alias lgnom='pushd $CCP4_MASTER/laue/gnom>/dev/null'
    alias lgnoms='pushd $CCP4_MASTER/laue/gnom/src>/dev/null'
    alias lbin='pushd $CBIN>/dev/null'

  fi

# Set-up cctbx environment
test -r $CCP4/lib/cctbx/cctbx_build/setpaths.sh && . $CCP4/lib/cctbx/cctbx_build/setpaths.sh

# Set-up phaser environment
#if ( test -d $CCP4/src/phaser) ; then
#  phaser_mtype=`$CCP4/src/phaser/bin/machine_type`
#  phaser_version=`grep PHASER_VERSION $CCP4/src/phaser/conf/version.sh | awk '{print $3}'`
#  phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh"
#  test -r $phaser_setup_file && . $phaser_setup_file
#fi

### BALBES root configuration
if ( test -d $CCP4/share/BALBES/Package)
then
  export BALBES_ROOT=$CCP4/share/BALBES/Package
fi

# Test for ARP/wARP 7.3 and source
if ( test -f ${CCP4_MASTER}/arp_warp_7.3/arpwarp_setup.bash )
then
   . ${CCP4_MASTER}/arp_warp_7.3/arpwarp_setup.bash
fi