Michael Schmitz wrote:
>> Christoph Gartmann (GARTMANN at IMMUNBIO.MPG.DE) wrote:
> : Hello,
>> : I think this question has been addressed before but I couldn't find it anymore.
> : So, is it possible to use the LookUp indices provided by GCG under SRS V4.08?
> : If so, how?
>> As far as I remember, the problem discussed before was the opposite: using
> existing SRS-build indices with Lookup. And that required changes to Lookup ...
>> Michael Schmitz
Hello,
I don't remember the precise patch either, and as I moved to another site I had to do it again; admittedly I restrict this posting to UNIX by now. There are three problems with srs4_08 in GCG 8.1:
1) the GCG version is << 4.08
2) it can do only sequence libraries
3) building in GCG is not too trivial as it uses a complex makefile
The strategy to make it work is as follows. I appreciate any feedback.
Regards
Reinhard
1) MAKE NORMAL NATIVE SRS
=================================
Get srs4.08 and treat it as usual. Make sure that getz -libs gets you at least a single "sequence" type.
% getz -libs
Library Group Entries Index Date
-------------------------------------------------------------------
SWISSPROT Sequence 52205 4/25/96
SWISSNEW Sequence 2819 4/25/96
PIR Sequence 82066 4/25/96
NRL3D Sequence 6063 4/26/96
...
2) MAKE A NEW DIRECTORY AND GET THE GCG STUFF WORKING
=============================================================
Make a new directory, move there, invoke GCG and GCGSUPPORT, and get gensource:lookup.c as usual:
% fetch gensource:lookup.c
Fetch copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
lookup.c
Next, get the makefiles (fetch make*) and change the "name" c example
in makefile.mm to "lookup". Make the makefile. The next is a crude
hack and the GCG folks might correct me but this worked in my hands.
Next, printenv the variable for the executable
% printenv SRSEXE
Edit the makefile and add the variable you got there (e.g. /sw/srs4_08/bin/irix) and add this to the 'include' section
_before_ the other includes (this is extremely important as you will
use GCVG's include otherwise). In my system this might look like
CFLAGS = -Dirix -Dunix -D__LONGLONG -ansiposix -cckr -common $(DEBUGFLAGS) -I/sw/srs4_08/bin/irix -I$(IDIR)
Do the same with the link library statement and add the need to add libsrs.a from your native SRS installation.
CEXLIBS = -L/sw/srs4_08/bin/irix/ -lsrs -L$(LDIR) -lgenshare -l$(CURSES) -lm -lmalloc
(remember that this must look different on your system as you will have the srs installation in a different path! Also, do not allow any space between -I and -L and the leading slash of the filename).
Try it - don't get frustrated as it won't work but you should get something like
% make lookup
cc -Dirix -Dunix -D__LONGLONG -ansiposix -cckr -common -DNDEBUG -I/sw/srs4_08/bin/irix/ -I/bio1/gcg/gcg81/gcgsource/include -c lookup.c
cc -DNDEBUG lookup.o /bio1/gcg/gcg81/gcgbin/oblib/libapp.a -L/sw/srs4_08/bin/irix/ -lsrs -L/bio1/gcg/gcg81/gcgbin/oblib -lgenshare -lcurses -lm -lmalloc -o lookup
ld:
Unresolved:
MsgGetFnct
*** Error code 1
3. MODIFY LOOKUP TO RUN ONLY SEQUENCE LIBRARIES
===================================================
There are only three locations which you need to change.
% diff lookup.c.patch lookup.c.orig
568a571
> if (!strcmp(g->com, "Sequence")) {
582c585
<
---
> }
1702a1706,1712
>> static int (*PrintMessage)(MSGo *) = NULL; /* pointer to print function */
>> INT4 (*MsgGetFnct (void))()
> {
> return PrintMessage;
> }
The first is that in line 568 there is a loop which embraces all
libraries. That's not what we need, as we got the group in the
previous line the statement
for(lcontext = 0; l = LibNextLib(g, &lcontext);
needs only be executed if g->com is "sequence":
571 for(lcontext = 0; l = LibNextLib(g, &lcontext); ) {
(gdb) p g
$3 = (struct SRSoGROUP_ *) 0x10266404
(gdb) p *g
$4 = {key = 0x1028033c "S", com = 0x10280330 "Sequence", short_nm = 0x10280340 "SQ",
cmnt = 0x10280344 "Search sequence libraries", help = 0x10280360 "srs_me query lib",
single_f = 0 '\000', library = {0x10264228, 0x102642c4, 0x102645d0, 0x10264360, 0x102643fc, 0x10264498,
0x10264708, 0x10265c5c, 0x10265cf8, 0x0 <repeats 16 times>}, libraryN = 9, df_t = {0x102784ac,
0x10278484, 0x102784d4, 0x10278524, 0x1027854c, 0x10278574, 0x1027859c, 0x102785c4, 0x102785ec,
0x1027868c, 0x10278664, 0x10278614, 0x1027863c, 0x102784fc, 0x102786dc, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0,
0x0, 0x0, 0x0, 0x0}, upd_f = 0 '\000'}
All what we do, therefore, is add the line
if (!strcmp(g->com, "Sequence")) {
before this line (after the line stating SLBo *l;) and end this
condition just before the end of the main loop (stating
} /* end loop */) with a single }.
This passage should now look like
for(count = 0, gcontext = 0; g = LibNextLibGroup(&gcontext);) {
int lcontext;
SLBo *l;
if (!strcmp(g->com, "Sequence")) {
for(lcontext = 0; l = LibNextLib(g, &lcontext); ) {
[... some lines deleted deleted for clarity ...]
if(!access(buf, R_OK))
activeLib[count++] = l;
}
}
} /* end loop */
If you want to be really perfect and have more than 24 sequence libraries :-) you need to add a counter that tells the LibNextLib
to stop after 23 readings but you'll miss all beyond this point.
4. ADD THE MISSING FUNCTION
===============================
Last, we need to add the function MsgGetFnct and define PrintMessage
as this got dropped at least in my 4.08 SRS native version.
Append the lines
static int (*PrintMessage)(MSGo *) = NULL; /* pointer to print function */
INT4 (*MsgGetFnct (void))()
{
return PrintMessage;
}
to lookup.c, exit the editor, and recompile with "make lookup".
Try it out:
% ./lookup
LookUp identifies sequences by name, accession number, author, organism,
keyword, title, reference, feature, definition, length, or date. The output
is a list of sequences.
The LookUp program is experimental in this release--please look carefully at
your results.
LOOKUP in what sequence libraries:
a) swissprot
b) swissnew
...
m) All libraries
n) quit
Please choose one or more (* m *):
5. RETURN THE BINARY TO THE USUAL PLACE
============================================
Last, you need to copy the binary to the usual place
% mv $GCGUTILDIR/lookup $GCGUTILDIR/lookup.orig
% cp lookup $GCGUTILDIR/lookup
and rescue the source code.
DISCLAIMER
==========
No warranty for this patch. This is an inofficial fix and
neither myself nor GCG or my employer are responsible for
this posting or any consequence arising thereof.
[PS: Please don't use this message to reply:to as I don't read my mailbox
at this address frequently. I've posted from my new address once earlier
and you can get the mail address from there if you need]
--
Reinhard Doelz, Basel, Switzerland
