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