144 lines
3.5 KiB
Text
144 lines
3.5 KiB
Text
#
|
|
# Setup file for Staden software running on a Sun
|
|
# This setup for Bourne shell (sh) users
|
|
#
|
|
# This file should be source'd from your .profile
|
|
# assuming the environmental variable STADENROOT has been set up
|
|
# to point to the root directory for the staden software
|
|
#
|
|
# e.g.
|
|
# STADENROOT=/home/BioSW/staden; export STADENROOT
|
|
# . $STADENROOT/staden.setup
|
|
#
|
|
#
|
|
#echo 'Setting up the Staden software environment...'
|
|
|
|
PATH=$PATH:$STADENROOT/bin; export PATH
|
|
|
|
STADTABL=$STADENROOT/tables; export STADTABL
|
|
STADUSER=$STADENROOT/userdata; export STADUSER
|
|
STADHELP=$STADENROOT/help; export STADHELP
|
|
|
|
|
|
#
|
|
# files for nip
|
|
#
|
|
ECRIBS=$STADTABL/PERCPTRON.WTS; export ECRIBS
|
|
EUKRIBS=$STADTABL/RIBSEUKAR.WTS;export EUKRIBS
|
|
INTRONS=$STADTABL/INTRON.WTS; export INTRONS
|
|
ECPROMS=$STADTABL/PROKPROMS.WTS;export ECPROMS
|
|
RENZYM4=$STADTABL/RENZYM.4; export RENZYM4
|
|
RENZYM6=$STADTABL/RENZYM.6; export RENZYM6
|
|
RENZYMAL=$STADTABL/RENZYM.ALL; export RENZYMAL
|
|
HELPNIP=$STADHELP/nip_help; export HELPNIP
|
|
NIPHELP=$STADHELP/NIP.HLP; export NIPHELP
|
|
NIPHPNT=$STADHELP/NIP.PNT; export NIPHPNT
|
|
NIPMARG=$STADTABL/NIP.MRG; export NIPMARG
|
|
|
|
#
|
|
# files for sip
|
|
#
|
|
HELPSIP=$STADHELP/sip_help; export HELPSIP
|
|
SIPHELP=$STADHELP/SIP.HLP; export SIPHELP
|
|
SIPHPNT=$STADHELP/SIP.PNT; export SIPHPNT
|
|
SIPMARG=$STADTABL/SIP.MRG; export SIPMARG
|
|
PROTMAT=$STADTABL/PROTMAT.DAT; export PROTMAT
|
|
|
|
#
|
|
# files for sap
|
|
#
|
|
HELPSAP=$STADHELP/sap_help; export HELPSAP
|
|
SAPHELP=$STADHELP/SAP.HLP; export SAPHELP
|
|
SAPHPNT=$STADHELP/SAP.PNT; export SAPHPNT
|
|
SAPMARG=$STADTABL/SAP.MRG; export SAPMARG
|
|
|
|
#
|
|
# files for bap
|
|
#
|
|
HELPBAP=$STADHELP/bap_help; export HELPBAP
|
|
BAPHELP=$STADHELP/BAP.HLP; export BAPHELP
|
|
BAPHPNT=$STADHELP/BAP.PNT; export BAPHPNT
|
|
BAPMARG=$STADTABL/BAP.MRG; export BAPMARG
|
|
|
|
#
|
|
# files for dap
|
|
#
|
|
HELPDAP=$STADHELP/dap_help; export HELPDAP
|
|
DAPHELP=$STADHELP/DAP.HLP; export DAPHELP
|
|
DAPHPNT=$STADHELP/DAP.PNT; export DAPHPNT
|
|
DAPMARG=$STADTABL/DAP.MRG; export DAPMARG
|
|
TAGDB=$STADTABL/TAGDB; export TAGDB
|
|
|
|
#
|
|
# files for pip
|
|
#
|
|
PIPMARG=$STADTABL/PIP.MRG; export PIPMARG
|
|
PROTGRP=$STADTABL/PROTEIN.GRP; export PROTGRP
|
|
PROTALL=$STADTABL/PROTEIN.ALL; export PROTALL
|
|
ROBSON=$STADTABL/ROBSON.WTS; export ROBSON
|
|
HELPPIP=$STADHELP/pip_help; export HELPPIP
|
|
PIPHELP=$STADHELP/PIP.HLP; export PIPHELP
|
|
PIPHPNT=$STADHELP/PIP.PNT; export PIPHPNT
|
|
|
|
#
|
|
# files for mep
|
|
#
|
|
MEPMARG=$STADTABL/MEP.MRG; export MEPMARG
|
|
HELPMEP=$STADHELP/mep_help; export HELPMEP
|
|
MEPHELP=$STADHELP/MEP.HLP; export MEPHELP
|
|
MEPHPNT=$STADHELP/MEP.PNT; export MEPHPNT
|
|
|
|
#
|
|
# files for rep
|
|
#
|
|
ALUNAMES=$STADTABL/alus/files; export ALUNAMES
|
|
|
|
|
|
#
|
|
# miscellaneous files
|
|
#
|
|
GIPMEM=$STADHELP/gip_help; export GIPMEM
|
|
HELPSTADEN=$STADHELP/staden_help;export HELPSTADEN
|
|
|
|
#
|
|
# vector sequences
|
|
#
|
|
M13MP18_VECTOR=$STADUSER/m13mp18.vec; export M13MP18_VECTOR
|
|
PUC18_VECTOR=$STADUSER/puc18.vec; export PUC18_VECTOR
|
|
BLUE_VECTOR=$STADUSER/blue.vec; export BLUE_VECTOR
|
|
|
|
|
|
|
|
#
|
|
# Sequence databases (currently embl cdrom format only)
|
|
#
|
|
|
|
# The file SEQUENCELIBRARIES lists the available libraries
|
|
# and the *DESCRP files contain the names of each libraries files
|
|
#
|
|
SEQUENCELIBRARIES=$STADTABL/SEQUENCELIBRARIES; export SEQUENCELIBRARIES
|
|
EMBLLIBDESCRP=$STADTABL/EMBLLIBDESCRP; export EMBLLIBDESCRP
|
|
SWISSLIBDESCRP=$STADTABL/SWISSLIBDESCRP; export SWISSLIBDESCRP
|
|
|
|
|
|
#
|
|
# Help X11 find where things are
|
|
#
|
|
XFILESEARCHPATH=$STADHELP/%N%S:$STADTABL/%N%S:${XFILESEARCHPATH-/usr/lib/X11/%T/%N%S}
|
|
export XFILESEARCHPATH
|
|
|
|
#
|
|
# Find manual pages
|
|
#
|
|
MANPATH=${MANPATH-/usr/man}:$STADENROOT; export MANPATH
|
|
|
|
#
|
|
# For gip, specify default digitizer port
|
|
#
|
|
DIGITIZER=/dev/ttyb; export DIGITIZER
|
|
|
|
#
|
|
# Sequence databases
|
|
#
|
|
|
|
. $STADTABL/libraries.config.sh
|