EMBOSS under Mac OS-X ?

Frank M. Mattes mattes at rfhsm.ac.uk
Mon May 14 08:00:58 EST 2001


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
>
> ---
>






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