EMBOSS - Indexing breaks on large databases

jrvalverde at cnb.uam.es jrvalverde at cnb.uam.es
Thu Feb 8 09:00:49 UTC 2001

"Len F. Zaifman" <leonardz at bioinfo.sickkids.on.ca> wrote:
> I have installed emboss 1.9.1 on an O2000. It installed nicely once I
> gave up on installing it shared.

BTW, I have succeeded in compiling EMBOSS for IRIX using 64 bit

It required some tweaking, but works. The recipe for those willing to
give it a try is

	- remove 'gcc' from your path
	- define COMPILER_DEFAULTS_PATH appropriately (see pe_environ)
	to look for a compiler.defaults file containing e.g.
	- ./configure in EMBOSS and all EMBASSY subdirs
	- search in all files for 'CC = cc' and substitute it
	for 'CC = cc -64'
	- same for 'LD = /bin/ld' -> 'LD = /bin/ld -64'
	- make

The reason is that compiling depends on the Makefile and on libtool,
as well as linking. I didn't spend much in looking at configure since
the above steps where so straightforward. I know I should look into
the configure script and add an option for 64-bit-irix-compile or some
such, but that'll have to wait till I have time for it.

Yes, I know, the search and substitute thing looks tedious, but it
isn't, honest: create a 'chfile.sh' out of the EMBOSS source hierarchy

cp $1 $1.orig
mv $1 tmpfile
sed -e 's/CC="cc"/CC="cc -64"/g' $1 > tmpfile
sed -e 's/CC = cc/CC = cc -64/g' $1 > tmpfile
sed -e 's/\/bin\/ld/\/bin\/ld -64/g' $1 > tmpfile
rm tmpfile
## if you are sure, uncomment this 
#rm $1.orig

'cd' to the emboss directory and run

	find . -type f -exec /path/to/chfile.sh {} \; -print

and you are done with the CC changes. Libtool requires special 
treatment since it uses quotes


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