new release srs5.03

Thure Etzold etzold at embl-heidelberg.de
Sat Oct 12 07:20:49 EST 1996


A new release of srs5 is ready and can be ftp'ed from

ftp://felix.embl-heidelberg.de/pub/databases/trembl/srs5_03b.tar.gz

I append here the release notes

regards
Thure

--------------------------------------------------------------------
SRS release 5.03b
=================

This is the beta release of SRS 5.0 which has been compiled and tested
on
IRIX 5.x, IRIX 6.x (32-bit binary), OSF1 2.x, 3.x, 4.x, Linux 2.x and
ULTRIX 4.x. It could also work on AIX, HP-UX, IRIX 6.x (64-bit binary),
Solaris, SunOS.

If installing on Linux, you will have no csh and so you should remove
the -e
flag on the first line of the file srs/srsinstall.

First a list of what is still missing:

  1) the GCG formatted databanks are still not supported
  2) extraction of subentries (eg, sequence features) is not
     yet possible

Both items are being worked on and will be hopefully released in the
next
version which will then be without the 'b'.

Now the new things:
===================

1) The .is files can now run as an independent script and used by
   SRS without changing the script.
   So in 'tfsite.is' the 'entry' production must always have
$In:[file:text]
   
   entry:   ~ {$In:[file:text] $Out}
              ('AC' {$Not} ln)*
              ('AC  ' {$entryFip=$Fip $Wrt} ln {$App} 
               ('AC' {$Not} ln {$App})+)?
            ~
   
   and the code for testing at the end must use "$TestMode" 
   
   
   if:$TestMode {
     $job = $JobNew:[prod:$rules skip:" "
fileName:'/data/transfac/site.dat']
     while:$JobTokens:[$job name:id print:1] {
       $JobNext:$job
       $print:"-------->entry\n" 
     }
   }
   
2) There is now a very simple Icarus debugger. It is by no means ready
but
   even at this stage really useful. It is documented in chapter 6 in
the
   WWW manual. 
   
3) I modified the information pages for databanks and data-fields in 
   SRSWWW. Have a look at .it files in 'SRSDB:' which have the
description
   about the databanks and fields which is placed into these pages.
   The library information page has the links to the .i, .it, .is
   files for each databank (btw, our test server is 
   'http://kappa.embl-heidelberg.de:8000/srs/'). The idea is that every 
   databank should be documented by a .it file.
   
4) There is an emacs lisp file in 'SRSETC:' which defines an Icarus mode
-
   defines only coloring with fontlock. I don't know enough emacs lisp
to wri
   a proper mode with automatic indentation etc. - any volunteers?
   
5) The indexing of databank partitions runs stable now. This means that
   big databanks like genbank and EMBL can be indexed in chunks of eg, 
   100000 entries and then later merged. srscheck takes care of all
   necessary commands. Have a look in embl.i: attribute 'partSize' of 
   $library sets the partitioning. With a part size of 100000 the
indexing
   of EMBL on an alpha takes less than 50mbyte memory.


--

Thure Etzold, etzold at embl-heidelberg.de
Johnathon Weare, weare at embl-heidelberg.de
10. October, 1996


-- 
===============================================================================
Thure Etzold                                   | EMBL
E-mail: etzold at embl-heidelberg.de              | Postfach 10.2209
Tel: (49) 6221 387529                          | 69012 Heidelberg
Fax: (49) 6221 387517                          | Germany




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