EasyGene 1.2		INSTALLATION INSTRUCTIONS


   DESCRIPTION

   EasyGene v. 1.2 predicts genes in sequences of prokaryotic DNA. The method
   is described in detail in the following articles:

   EasyGene 1.2 (this version):

   Large-scale prokaryotic gene prediction and comparison to genome
   annotation.
   Pernille Nielsen and Anders Krogh.
   Bioinformatics 21(24):4322-4329, 2005.

   EasyGene 1.1 (original version):

   EasyGene - a prokaryotic gene finder that ranks ORFs by statistical
   significance.
   Thomas Schou Larsen and Anders Krogh.
   BMC Bioinformatics 4:21, 2003.

   More information on the method is also available at:

   	http://www.cbs.dtu.dk/services/EasyGene/
   	http://www.binf.ku.dk/cgi-bin/easygene/search/


   DOWNLOAD

   By special agreement only; contact software@cbs.dtu.dk for details.


   PRE-INSTALLATION

   The version 1.2 requires  Linux, PERL 5.6 or better  and NCBI BLAST 2.2.11
   or better. The software package consists of two files:

       easygene-1.2.readme         this file
       easygene-1.2.Linux.tar.Z    compressed TAR archive

   After installation the software will occupy less than 300 Mb of diskspace.


   INSTALLATION

   1. Uncompress and untar the package:

        cat easygene-1.2.Linux.tar.Z | uncompress | tar xvf -

      This will produce a directory 'easygene-1.2'.

   2. In the 'easygene-1.2' directory edit the main script 'easygene'. In the
      part of the script marked "GENERAL SETTINGS: CUSTOMIZE ... "  configure
      the following variables:

        EG            full path to the 'easygene-1.2' directory

        AWK	      full path to 'awk' e.g. /usr/bin/gawk
        PERL	            "	   'perl'
        BLASTALL            "	   'blastall' (NCBI BLAST)
        FORMATDB            "	   'formatdb' (NCBI BLAST)

   3. In the 'easygene-1.2/lib/sprot' directory remove the files:

        reldate.txt
	sprot.dat

      Create the files again as symbolic links to the files 'reldate.txt' and
      'uniprot_sprot.dat'  in the flat file UniProt distribution available on
      your system. If you do not have UniProt installed in flat file form you
      can download the two files mentioned above from  e.g. ftp.expasy.ch, in
      '/databases/uniprot/current_release/knowledgebase/complete/'.  In  such
      case they may be placed in 'easygene-1.2/lib/sprot' directly.  Remember
      to uncompress the 'uniprot_sprot.dat.gz' file.

      Please note the difference in  file name:  'uniprot_sprot.dat'  must be
      installed or linked as 'sprot.dat'.

      In the 'easygene-1.2' directory verify the status of the database:

        > ./easygene -db stat

      The presence of the database should be reported; y ou need to format it
      for EasyGene:

        > ./easygene -db update

      Verify the status again:

        > ./easygene -db stat

      The presence of both databases should be reported now.

   4. Make sure that the 'easygene-1.2/new_trainruns' directory has the right
      permissions: the listing should read "drwxrwxrwt ..." (sticky bit set).
      If the sticky bit is not set, set it:

        > chmod 1777 new_trainruns

      The directory contains an example directory 'BA02' with two input files
      for 'Buchnera aphidicola' provided:
      
        NC_004061.fna (genome sequence in FASTA, mandatory)
        NC_004061.gbk (GenBank entry, optional)

      It is possible to download the complete results of a training  for that
      organism, for comparison with own runs in the future:

        http://www.cbs.dtu.dk/services/EasyGene/BA01.tar.gz

   5. a. Copy the 'easygene' script  to a directory in the users' path.
      b. copy the  'discotope.1' file to  a location  in your manual system.

   6. Enjoy ...


   PROBLEMS

   Contact support@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the method should be sent to Thomas
   Schou Larsen, thomas@biopeople.dk.

   2010-12-13