159 lines
3.3 KiB
Plaintext
159 lines
3.3 KiB
Plaintext
#
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# Setup file for Staden software running on a Sun
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# This setup for c-shell (csh) users
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#
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# This file should be source'd from your .login
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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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# setenv STADENROOT /home/BioSW/staden
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# source $STADENROOT/staden.login
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#
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#
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#echo 'Setting up the Staden software environment...'
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set path = ($path $STADENROOT/bin)
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setenv STADTABL $STADENROOT/tables
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setenv STADUSER $STADENROOT/userdata
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setenv STADHELP $STADENROOT/help
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# The default is 'vi' but this causes the X versions to hang
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setenv SEQEDT 'xterm -e vi'
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#
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# files for nip
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#
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setenv ECRIBS $STADTABL/PERCPTRON.WTS
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setenv EUKRIBS $STADTABL/RIBSEUKAR.WTS
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setenv INTRONS $STADTABL/INTRON.WTS
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setenv ECPROMS $STADTABL/PROKPROMS.WTS
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setenv RENZYM4 $STADTABL/RENZYM.4
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setenv RENZYM6 $STADTABL/RENZYM.6
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setenv RENZYMAL $STADTABL/RENZYM.ALL
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setenv HELPNIP $STADHELP/nip_help
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setenv NIPHELP $STADHELP/NIP.HLP
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setenv NIPHPNT $STADHELP/NIP.PNT
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setenv NIPMARG $STADTABL/NIP.MRG
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# files for nipf
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setenv NIPFMARG $STADTABL/NIPF.MRG
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#
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# files for sip
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#
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setenv HELPSIP $STADHELP/sip_help
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setenv SIPHELP $STADHELP/SIP.HLP
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setenv SIPHPNT $STADHELP/SIP.PNT
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setenv SIPMARG $STADTABL/SIP.MRG
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setenv PROTMAT $STADTABL/PROTMAT.DAT
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#
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# files for sap
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#
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setenv HELPSAP $STADHELP/sap_help
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setenv SAPHELP $STADHELP/SAP.HLP
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setenv SAPHPNT $STADHELP/SAP.PNT
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setenv SAPMARG $STADTABL/SAP.MRG
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#
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# files for bap
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#
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setenv HELPBAP $STADHELP/bap_help
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setenv BAPHELP $STADHELP/BAP.HLP
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setenv BAPHPNT $STADHELP/BAP.PNT
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setenv BAPMARG $STADTABL/BAP.MRG
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#
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# files for dap
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#
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setenv HELPDAP $STADHELP/dap_help
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setenv DAPHELP $STADHELP/DAP.HLP
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setenv DAPHPNT $STADHELP/DAP.PNT
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setenv DAPMARG $STADTABL/DAP.MRG
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setenv TAGDB $STADTABL/TAGDB
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#
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# files for pip
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#
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setenv PIPMARG $STADTABL/PIP.MRG
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setenv PROTGRP $STADTABL/PROTEIN.GRP
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setenv PROTALL $STADTABL/PROTEIN.ALL
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setenv ROBSON $STADTABL/ROBSON.WTS
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setenv HELPPIP $STADHELP/pip_help
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setenv PIPHELP $STADHELP/PIP.HLP
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setenv PIPHPNT $STADHELP/PIP.PNT
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#
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# files for mep
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#
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setenv MEPMARG $STADTABL/MEP.MRG
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setenv HELPMEP $STADHELP/mep_help
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setenv MEPHELP $STADHELP/MEP.HLP
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setenv MEPHPNT $STADHELP/MEP.PNT
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#
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# files for rep
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#
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setenv ALUNAMES $STADTABL/alus/files
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#
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# miscellaneous files
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#
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setenv GIPMEM $STADHELP/gip_help
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setenv HELPSTADEN $STADHELP/staden_help
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#
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# Typing "staden" will list all the program names
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#
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alias staden 'cat $STADHELP/stadenp_help'
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#
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# vector sequences
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#
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setenv M13MP18_VECTOR $STADUSER/m13mp18.vec
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setenv PUC18_VECTOR $STADUSER/puc18.vec
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setenv BLUE_VECTOR $STADUSER/blue.vec
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setenv PROSITE /pubseq/pubseq/seqlibs/prosite
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setenv PROSITENAMES /pubseq/pubseq/seqlibs/prosite/prosite.nam
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#
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# Help X11 find where things are
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#
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if ( $?XFILESEARCHPATH ) then
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setenv XFILESEARCHPATH ${STADHELP}/%N%S:${STADTABL}/%N%S:${XFILESEARCHPATH}
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else
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setenv XFILESEARCHPATH ${STADHELP}/%N%S:${STADTABL}/%N%S:/usr/lib/X11/%T/%N%S
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endif
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#
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# Find manual pages
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#
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if ( $?MANPATH ) then
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setenv MANPATH ${MANPATH}:${STADENROOT}
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else
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setenv MANPATH /usr/man:${STADENROOT}
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endif
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#
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# For gip, specify default digitizer port
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#
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setenv DIGITIZER /dev/ttyb
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#
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# Sequence databases
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#
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source $STADTABL/libraries.config.csh
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