Many thanks for the comperensive description who to build emboss under
Mac-OS X. Would it be possible to put the binaries for OS-X on one of the
ftp servers hosting other bionet software ?
Frank Mattes
Dept. of Virology
Royal Free and University College Medical School
London
"Don Gilbert" <gilbertd at bio.indiana.edu> wrote in message
news:200105122236.RAA29457 at cricket.bio.indiana.edu...
> In article <9dgdv0$b5u$1 at niobium.hgmp.mrc.ac.uk>,
> Frank M. Mattes <mattes at rfhsm.ac.uk> wrote:
> >this might be a silly question, but I'm not good and knowlegable enough
to
> >do it by myself. Has anybody compiled and set up the EMBOSS package under
> >Mac OS-X ?
>>> This is how I was able to build EMBOSS on MacOSX.
> I tested EMBOSS-1.0.1.tar.gz release of last fall
>> STEP 0
> if not done, install MacOSX developer CD package
>> STEP 1
> -- as root make cc compiler known as gcc (which it is)
> -- (this will make your life simpler installing gnu-based packages)
> cd /usr/bin
> ln cc gcc
>> STEP 2
> -- unpack EMBOSS-*.tar.gz somewhere
> gnutar -zxf EMBOSS-1.0.1.tar.gz
> cd EMBOSS-1.0.0
>> STEP 3
> -- edit configure file to fix some things
> -- configure -> ltconfig has problem with passing $host value
> -- remove -lX11 as constant (so --without-x works)
>> # fix ltconfig call so host is specified (some configure bug)
> << find
> $libtool_flags --no-verify $ac_aux_dir/ltmain.sh $host \
> >> change to
> $libtool_flags --no-verify $ac_aux_dir/ltmain.sh darwin \
>> << find
> if test "$no_x" = yes; then
> # Not all programs may use this symbol, but it does not hurt to define
it.
> cat >> confdefs.h <<\EOF
> #define X_DISPLAY_MISSING 1
> EOF
>> X_CFLAGS= X_PRE_LIBS= X_LIBS= X_EXTRA_LIBS=
> else
> >> add this X_LIBS=-lX11 line
> X_LIBS=-lX11
> if test -n "$x_includes"; then
> X_CFLAGS="$X_CFLAGS -I$x_includes"
> fi
>> << find
> XLIB="$X_LIBS -lX11 $X_EXTRA_LIBS"
> >> change to
> XLIB="$X_LIBS $X_EXTRA_LIBS"
>>> STEP 4
> -- configure and make. after above edits, the make worked
> ./configure --host=darwin --without-x
> make >& log.make &
>> STEP 5
> -- test some things
> emboss/getorf test/data/dna.genbank -outseq stdout
> emboss/pepstats test/data/prot.swiss -outfile stdout
>> -- try a graphic one
> setenv PLPLOT_LIB `pwd`/plplot/lib
> emboss/plotorf -graph ps test/embl/rod.dat
>> -- install in default /usr/local/... as root
> make install
>>> Notes:
>> -- you will need to fetch and install some standard data
> to use several programs (see emboss/data/)
>> -- w/o an X Window server, default graphics won't show up.
> Tenon(?) sells an Xwindow server for MacOSX
>> -- Don
>> --
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gilbertd at bio.indiana.edu>> ---
>
