[EMBnet ADMIN] Re: EMBOSS - Indexing breaks on large databases

[David Martin]

On Thu, 8 Feb 2001 jrvalverde at cnb.uam.es wrote:

> "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
> compilation.
>
> 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.
> 		:abi=64:isa=4:proc=r10k
> 	- ./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
> containing
>
> #/bin/sh
> 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

This will break if you have more than one ofthe sed commands run. It will
either overwrite the previous substitutions or die if noclobber is set.

put the sed commands in a file and source them with sed -f and it should
work.

alternatively

setenv CC "cc -64"; setenv LD "/bin/ld -64"; ./configure

may be easier (if configure is working properly).


>
> '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
>


..d

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