Newsgroups: bit.listserv.info-gcg
Date:         Tue, 6 Oct 1992 16:16:19 -0500
Reply-To:     hogan@GCG.COM
              <INFO-GCG@UTORONTO.BITNET>
From:         hogan@GCG.COM
Subject:      CHANGES TO ACCOMODATE THE NCBI VERSION OF GENBANK
Comments: To: info-gcg@utoronto.bitnet@gcg.com
Comments: cc: BUTLER@gcg.com, SMITH@gcg.com

If you plan to ftp GenBank release 73-1 from NCBI (ncbi.nlm.nih.gov) and format
it with the GCG utility GenBankToGCG, you will need to modify the GCG Package.
Below are the instructions for the VMS and UNIX platforms.

***************************  VMS  *******************************************
NCBI has included an additional sequence file containing information from the
NCBI backbone for this release only.  According to Dennis Benson of NCBI, this
file, named gbnlm.seq, is an interim file.  In future releases, the sequence
information in the backbone will be included in the appropriate GenBank
subsections.

Because of the interim status of this sequence file, the following
modifications should be made prior to ftp-ing and updating GenBank 73-1.
These modifications will have to be removed before the next GenBank release
(74) from NCBI in December.  Because these changes are interim, you may want to
make copies of GenSiteCom:SiteUserSpecs.Com, GenRunData:DBNames.Map,
GenRunData:GenData.Fil, GenRunData:GenBank.Farm, and GenRunData:GenEMBL.Farm
prior to modification.  The unmodified copies of these files can then be used
to format future releases of GenBank.

In the directory GensiteCom, modify the file SiteUserSpecs.Com to include
support for gbnlm.seq.  Execute the following commands:

        $ GCG
        $ GCGSupport
        $ To GenSiteCom
        $ Edit SiteUserSpecs.Com

             Add the following lines at the end of the file:

                $ Assign/NoLog  GenBankdir:GB_NLM                      GB_NLM
                $ Assign/NoLog  GenBankDir:GB_NLM                      GBNLM
                $ Assign/NoLog  GenBankDir:GB_NLM                      NLM

Next, move to the directory GenRunData.

        $ To GenRunData

Edit the file DBNames.Map

        $ Edit DBNames.Map

             Add the following line to the GenBank subdivisions section:

                gbnlm           gb_nlm      !genbank backbone

Edit the files GenData.Fil, GenBank.Farm, and GenEMBL.Farm

        $ Edit GenData.Fil

             Include the following line at the end of the file:

                gb_nlm

        $ Edit GenBank.Farm

             Include the following line at the end of the file:

                gb_nlm

        $ Edit GenEMBL.Farm

             Include the following line at the end of the file:

                gb_nlm

Remember that these changes are only necessary for release 73-1 of GenBank.
Release 74 will not require these modifications.
*************************  UNIX  *********************************************

NCBI has included an additional sequence file containing information from the
NCBI backbone for this release only.  According to Dennis Benson of NCBI, this
file, named gbnlm.seq, is an interim file.  In future releases, the sequence
information in the backbone will be included in the appropriate GenBank
subsections.

Because of the interim status of this sequence file, the following
modifications should be made prior to ftp-ing and updating GenBank 73-1.
These modifications will have to be removed before the next GenBank release
(74) from NCBI in December.  Because these changes are interim, you may want to
make copies of gensitescript:siteuserspecs, genrundata:dbnames.map,
genrundata:gendata.fil, genrundata:genbank.farm, and genrundata:genembl.farm
prior to modification.  The unmodified copies of these files can then be used
to format future releases of GenBank.

In the directory gensitescript, modify the file siteuserspecs to include
support for gbnlm.seq.  Execute the following commands:


        % gcg
        % gcgsupport
        % to gensitescript
        % vi siteuserspecs

                Add the following lines at the end of the file:

                   name -q -s GB_NLM            GenBankdir:gb_nlm
                   name -q -s GBNLM             GenBankDir:gb_nlm
                   name -q -s NLM               GenBankDir:gb_nlm

Next, move to the directory genrundata.

        % to genrundata

Edit the file dbnames.map

        % vi dbnames.map

                Add the following line to the GenBank subdivisions section:

                        gbnlm           gb_nlm      !genbank backbone

Edit the files gendata.fil, genbank.farm, and genembl.farm

        % vi gendata.fil

             Include the following line at the end of the file:

                gb_nlm

        % vi genbank.farm

             Include the following line at the end of the file:

                gb_nlm

        % vi genembl.farm

             Include the following line at the end of the file:

                gb_nlm


Remember that these changes are only necessary for release 73-1 of GenBank.
Release 74 will not require these modifications.

For further information contact

Genetics Computer Group                      Telephone: (608) 231-5200
575 Science Drive, Suite B                   FAX:       (608) 231-5202
Madison, WI  53711                           E-Mail:    Help@GCG.Com
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU