/cluster/data/genbank/.
    -keep is specified.
    gbBlat no longer needs to be modified to specify
    the ooc file.  It is now specified in the genbank.conf
    file.
    genbank.conf
         file.
    ssh is configure to
           not require a passphase.
      $db refers to the database being aligned.
           Substitute the actual database name (e.g. hg15).
      kent/src/hg/makeDb/genbank/
      hg of hg13) and the organism names
           used in GenBank needs to be defined.  This is done by editing
           genbank/src/lib/gbGenome.c and rebuilding the programs.  It maybe
           necessary to define multiple organism name mappings.  A list of 
           organism in GenBank/RefSeq, along with the count of cDNAs is in:
           /cluster/data/genbank/data/organism.lst
           
      cd to the top of the genbank source (kent/src/hg/makeDb/genbank/)
      make to test if the source builds
      make install-server to update /cluster/data/genbank/.
      markd
           to update the round-robin code.
      kent/src/hg/makeDb/genbank/etc/genbank.conf to 
           configure this databases.   Must set:
           $db.serverGenome
           $db.clusterGenome
           $db.lift
           $db.align.maxGapChrs and a lift file.
           Commit your changes and then go to the top of the genbank source tree and update the installed genbank etc files with:
           make etc-update
           
           
      ssh fileServerfileServer is the NFS server with
          /cluster/data/genbank/.
      cd /cluster/data/genbank$gbRoot.
      nice bin/gbAlignStep -initial $db&This will run the entire alignment process.
           The -initial option defaults several parameters for
           and initial alignment and prevents this alignment from blocking
           the automatic daily alignments.
           
           Warning: gbAlignStep and other GenBank do not currently accept options after
           the positional arguments (i.e. the databases).
           
           All output is saved in the log file.
If your organism has xeno ESTs enabled, it's a good idea to start out by aligning and loading just the the mRNAs, as this will go much faster. Two options control what is aligned:
-srcDb=name - Restrict the source
                  database to either genbank or refseq.
               -type=name - Restrict the type of sequence
                  processeed to either mrna or est.
                If anything fails, a subset of the tasks done by
              gbAlignStep script can be rerun after correcting
              the problem.  This is done using the
              -continue=subtask option with
              subtask is either
              
copy - continue with coping to the iserver,
              this skips extracting the sequences to align.
              run - Continue with parasol blat run.
              finish - finish, alignments, doing
              lifting and filtering.
              gbAlignStep with
              -continue=finish.   If parasol loses track of
              the jobs, one can use the parasol recover
              command to generate a new jobs file with the jobs
              that have not completed.
    nice bin/gbDbLoadStep -drop -initialLoad $db-drop option drops any existing GenBank or RefSeq
               tables before loading.
          -initialLoad option
               when loading the ESTs.
          etc/align.dbs.
          etc/hgwdev.dbs.
           make update-etc
          $gbRoot/etc/align.dbs.
      data/aligned/genbank.139.0/hg16/
           data/aligned/refseq.139.0/hg16/
           data/aligned/refseq.139.0/hg16/*/mrna.native.*
           data/aligned/refseq.139.0/hg16/*/est.*.xeno.*
           -srcDb and -type.
      -srcDb and -type options restrict
           the subset.  The organism category (native or xeno) isn't 
           specified.  Reloading of ESTs isn't supported, use -drop
           and -initialLoad instead.
          nice bin/gbDbLoadStep -reload -srcDb=genbank -type=mrna $db