SRS 4.x on OpenVMS

Michael Schmitz schmitz at comp.bioz.unibas.ch
Wed Jul 19 12:25:29 EST 1995


Peter Rice (pmr at sanger.ac.uk) wrote:
[discussion about installation of SRS on VMS deleted]
: Sounds like you have VAX Fortran and Thure has DEC Fortran.

The code is written in Fortran ??? Am _I_ glad ... :-)

: For EGCG I also have to worry about some of the compiler options between
: DEC C and VAX C.

The compiler options stuff had been discussed before 
(/stan=vaxc/align=whatever), I didn't worry about that. Is there a difference
between old DECC and newer versions that have obsoleted to specify the C 
runtime library on the linker command line ??
Anyway - making a prog depend on something that is never produced by the 
MMS build procedure must _indeed_ be called a special feature. (Flame off)

Seroiusly - to get back to the original question:

a) it can be compiled, linked and run under VMS (AXP flavor)
b) it produces index files that can be read by getz to do reasonable
   work (remember Murphy)
c) if you run it on a VMS box, be sure you either get _huge_ page file quota 
   and WSQuota - or use srscheck -s 1000 as a fallback :-(
   Due to quota limitatios in Basel, I had to do all real work in my old lab
   in Duesseldorf - thanx to the colleagues there - where I needed about 
   100000 pgflquo on an outdated version of the EMBL database. Does 
   anybody know how the virtual memory requirements scale with database 
   sizes ?? ( the -s 1000 switch even worked at Basel URZ )

Does that answer Rodrigo's question (sorry I'm late with this answer, but
I started workin on this just monday afternoon) ??

And let me add a novice's question: we tried to incorporate a embl-to-
medline link by adding the following to embl.sdl:

------------------------------------------------------------------------------

    #field /gblid=%EMBL_RX_FIELD
           /itype=key /ftype=@DF_EMBL_MEDLINELINK /idtype=@SRSxSEQID
           /find="medlineid" /begstr="RX   "/nextstr="RX   "
           /relIndexSize=0.5 /isSystem=1

 
#link /id=%EMBL_MEDLINE
      /lib1=@EMBL_DB /lib2=@MEDLINE_DB /type=index
      /field1=@EMBL_RX_FIELD /field2=@MEDLINE_ID_FIELD
      /idtype1=@SRSxSEQID /idtype2=@ENTRY_ID

#srsfield /id=%DF_EMBL_MEDLINELINK
          /shortname="RX" /name="MedlineLink" /key="K"


and to hyperlink.sdl

#hyperlink /field=@EMBL_RX_FIELD
    /parse=embl_medline /parser=@INSERTLINK_PARSER
 
(if that wasn't present before; I don't know)

------------------------------------------------------------------------------

What I got was the following error after gnawing thru the whole database:

e__filopenerr, file could not be opened
"srsinx:embl_rx"

I feel this should tell me something - but what ??

Thanx in advance,

	Michael Schmitz
	BioComputing Basel




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