NetCTL 1.2               INSTALLATION INSTRUCTIONS


   DESCRIPTION

   NetCTL 1.2 software predicts CTL epitopes in protein sequences integrating
   prediction of peptide MHC binding, proteasomal C terminal cleavage and TAP
   transport efficiency.  The method is described  in detail in the following
   articles:

   NetCTL 1.2 (this version):

   Large-scale validation of methods for cytotoxic T-lymphocyte epitope
   prediction.
   Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, and Nielsen M.
   BMC Bioinformatics, 8:424, 2007.

   Original NetCTL paper:

   An integrative approach to CTL epitope prediction. A combined algorithm
   integrating MHC-I binding, TAP transport efficiency, and proteasomal
   cleavage predictions.
   Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O
   and Nielsen M.
   European Journal of Immunology, 35(8):2295-303, 2005.

   More information about the method can be found at:
   
       http://www.cbs.dtu.dk/services/NetCTL/


   DOWNLOAD

   Academic users:

       http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netCTL
   
   Other users:

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


   PRE-INSTALLATION

   NetCTL 1.2  will run  on the most common UNIX platforms  e.g. Linux, SunOS
   etc. The package consists of two files:
  
      netCTL-1.2.readme           this file
      netCTL-1.2.<unix>.tar.Z     compressed TAR archive

   where 'unix' is the UNIX platform on which you are about to install. After
   installation the software will occupy less than 10 Mb of diskspace.


   INSTALLATION

   1. Uncompress and untar the package:

      cat netCTL-1.2.<unix>.tar.Z | uncompress | tar xvf -

      This will produce a directory 'netCTL-1.2'.

   2. In the script  'netCTL' in that directory  locate  the section starting
      with "GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE".  Set the following two
      variables:

      CTLHOME   full path to the 'netCTL-1.2' directory on your system
      TMPDIR    e.g. /var/tmp

      Make sure  that TMPDIR has the sticky bit set  (the long listing should
      render 'drwxrwxrwt ...'). If not, set it:

      chmod 1777 $TMPDIR

      The setting of the variables  UNIX and AR  should not be changed unless
      the 'uname' program on your system is not standard.

   3. In the 'netCTL-1.2' directory test the software:

      ./netCTL test/test.fsa > test.out

      The result file 'test.out' should only differ  from the file 'test.out'
      in 'netCTL-1.2/test' in the site specific file system location details.

   4. a. Copy or link the 'netCTL' script to a directory in the users' path.

      b. Copy the 'netCTL.1' file to a location in your manual system. If you
         need a compiled version try running:

         man -d netCTL.1 | compress >netCTL.Z

         or:

         neqn netCTL.1 | tbl | nroff -man | col | compress >netCTL.Z

   5. Enjoy ...


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the NetCTL method should be sent to
   Morten Nielsen, mniel@cbs.dtu.dk.

   CBS, 7 Mar 2008
   K. Rapacki