IUBio

Some suggestions

Rodrigo Lopez rodrigol at bioslave.uio.no
Thu Mar 9 06:49:12 EST 1995


Dear SRS fans,

------------------------------------------------------------------
WARNING !  This posting contains some SRS specific technical
configuration info (not very advanced though). It is primarily meant
for the SRS administrators out there and not for the SRS user.
------------------------------------------------------------------

Now that we have a news group, Peter Rice and I decided to share
with you some additions to SRS which might be worth considering
applying at your site. We flipped a coin and I lost :-) So here
is some info we hope you will find usefull.



*********PERL SCRIPT TO REFORMAT GENEMAP INTO MIMMAP.DAT***********

The first of these is a tiny PERL program to produce the MIMMAP
database (it's really simply PERL):

ftp://ftp.no.embnet.org/pub/srs/scripts/genemap2dat.pl

The genemap database can be obtained via anonymous ftp from

ftp://ftp.gdb.org/omim/genemap

Then simply run the perl script:

% genemap2dat > mimmap.dat

Edit the file $SRSROOT/odd/srsdb.sdl and uncomment the line pertaining
to this database being present on your system. Add the location of
the file.

srsdb.sdl relevant sections for mimmap:

include "SRSSDL:medline.sdl"

#environmet /name=unix
...
    #libenv /lib=@MIMMAP_DB     /dir="/usr2/datfiles/"
! add the location of the mimmap.dat file and make sure the line above is 
uncommented !

... 
#srsdb
...
    #libid /n=48 /library=@MIMMAP_DB
...

Then:

% setenv SRSADMIN
% source whereversrsrootis/etc/prep_srs
% srssection
% srscheck
% srsupdate

*****************************NEW GIFS**********************************


The second addition is updated gifs, specially for the gifmap. These
can be obtained from:

ftp://ftp.sanger.ac.uk/pub/pmr/srs/*.gif

Not only are these pictures updated, by they are smaller and thus
take shorter to load. Transparent-interlaced  versions may be found at:

ftp://ftp.no.embnet.org/pub/srs/gifs/*.gif

If you decide to use these gifs instead of the ones that come in the
distribution please remember to either edit your $SRSROOT/www/wgetz.script
and net.html files, or simply change the name of the files to those from
the distribution.


****************************NEW SRSWWWST.PL*****************************

The third addition is actually an attempt to standarise the way the
SRS servers present their database info. The feature we are aiming
at, and Peter will have to correct me if there are more, is the
release number of the databases. If you read the documentation carefully
you will discover that:

% srsbuild -rel '41.0' embl

actually sets the release number required to fill in the rest of the
table produced by the 'Databanks' link in the Main SRS Page. When quering
other SRS servers for their status, the release number can also be checked
IF it has been set as explained above.

To see what we mean check the 'Databanks' link at:

http://www.sanger.ac.uk/srs/srsc
and
http://www.sanger.ac.uk/srs/status.html

Where is the script?

ftp://ftp.sanger.ac.uk/pub/pmr/srs/srswwwst.pl
or
ftp://ftp.no.embnet.org/pub/srs/scripts/srswwwst.pl


Hope you find this info usefull,

Rodrigo:-)







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