EMBOSS on OS X

[David Martin]

On Thu, 12 Apr 2001, Jean-Christophe Ame wrote:

>

Thanks for the reply. I'm forwarding this to emboss-dev to see if they
want to pick it up.

I'll wait till my Mac arrives then try it.. and be prepared for a few more
questions.

..d

> Hi David,

>
>
> For MacOSX to compile EMBOSS you need:
>
> first in the configure file:
>
> 1. remove from the configure file all the -lnsl call, because Mac OSX
> doesn't recognise it (don't ask me why)
> 2. add dylib at this position: (this is for configure to recognize X
> windows - I use Xtools from TENON at http:// www.tenon.com)
>
>    if (xmkmf) >/dev/null 2>/dev/null && test -f Makefile; then
>      # GNU make sometimes prints "make[1]: Entering...", which would confuse us.
>      eval `${MAKE-make} acfindx 2>/dev/null | grep -v make`
>      # Open Windows xmkmf reportedly sets LIBDIR instead of USRLIBDIR.
>      for ac_extension in a dylib so sl; do
>        if test ! -f $ac_im_usrlibdir/libX11.$ac_extension &&
>          test -f $ac_im_libdir/libX11.$ac_extension; then
>          ac_im_usrlibdir=$ac_im_libdir; break
>        fi
>      done
>      # Screen out bogus values from the imake configuration.  They are
>      # bogus both because they are the default anyway, and because
>
> and
>
> do
>    for ac_extension in a dylib so sl; do
>      if test -r $ac_dir/lib${x_direct_test_library}.$ac_extension; then
>        ac_x_libraries=$ac_dir
>        break 2
>      fi
>    done
> done
> fi
>
> Then, you need to copy some config.* files from the system for
> configure to work:
>
> $ cp /usr/libexexec/config.x .
>
> I think the config.guess and config.sub must be updated in emboss.
>
> Then,
>
> $ ./configure
>
> $ make
>
> Also, MacOSX doesn't like the -lm library (it is included in the
> system). It needs to be removed in the configure files where it
> appears (I think in MSE's package). Otherwise it works very well.
>
> One time I succeeded in doing
> aclocal -I m4
> autoconf
> automake -a
> ./configure = -disable-shared
> make
>
> But, it doesn't work anymore as aclocal complains ???
>
> Hope that will well.
> Jean-Christophe
>
>
>
>
>
>
>
>
>
>
>
> >On Wed, 11 Apr 2001, Jean-Christophe Ame wrote:
> >
> >>  I have installed EMBOSS on MacOSX since the release of the public
> >>  beta ant it works like a charm. There is no problem installing it,
> >>  one needs just to remove -lnsl everywhere in the configure file.
> >
> >
> >Could you give me a detailed description and I will plug it in to the next
> >edition of the admin guide. ie. a step by step process. I don't have a Mac
> >yet (though I should be getting one soon).
> >
> >Maybe the EMBOSS developers could add a something to the configure script
> >to deal with OS X?
> >
> >..d
> >
> >
> >>  Jean-Christophe
> >>
> >>
> >>  >David Martin wrote (to the EMBOSS list):
> >>  >>
> >>  >>  Has anyone tried compiling and running EMBOSS on MacOS X yet? I can
> >>  >>  imagine this being very nice with the X interfaces (Colimate etc).
> >>  >
> >>  >And Richard Phelps wrote (to me personally):
> >>  >>
> >>  >>  How might I install emboss on Mac Os X??
> >>  >
> >>  >Well, personally, I think I've touched the keyboard of a Mac
> >>maybe five times
> >>  >in my life (they're not common here at all), so it's highly unlikely I'll
> >>  >have the pleasure of using MacOS X any time soon.
> >>  >
> >>  >However:
> >>  >
> >>  >- It would be interesting to know how easily an application with
> >>a relatively
> >>  >   GNUish installation process compiles and installs on OS X.  I would
> >>  >   personally be very interested in feedback.  (Shouldn't be too
> >>difficult by
> >>  >   all reports.)
> >>  >
> >>  >- Secondly, there is a project underway (though it's in its early
> >>stages yet)
> >>  >   to unify packaging systems across a number of BSD-based
> >>operating systems,
> >>  >   including OS X.  In fact, Wilfredo Sanches, the former design
> >>lead on OS X,
> >>  >   is a developer on this project.  Should their work come to
> >>fruition, it's
> >>  >   possible that the existing FreeBSD port could eventually serve
> >>as the basis
> >>  >   for installing EMBOSS on OS X as well.  :-)  See:
> >>  >
> >>  >     http://www.openpackages.org/
> >>  >
> >>  >-- Johann
> >>
> >>  --
> >>  ________________________
> >>  Jean-Christophe Amé, PhD
> >>  U.P.R. 9003 du CNRS - Cancérogénèse Et Mutagénèse Moléculaire Et Structurale
> >>  École Supérieure De Biotechnologie De Strasbourg
> >>  Pôle API
> >>  Boulevard Sébastien-Brant
> >  > 67400 Illkirch
> >  > France
> >  >
> >  > tel.: 03 90 24 47 05
> >  > Fax.: 03 90 24 46 86
> >  >
>
> --
> ________________________
> Jean-Christophe Amé, PhD
> U.P.R. 9003 du CNRS - Cancérogénèse Et Mutagénèse Moléculaire Et Structurale
> École Supérieure De Biotechnologie De Strasbourg
> Pôle API
> Boulevard Sébastien-Brant
> 67400 Illkirch
> France
>
> tel.: 03 90 24 47 05
> Fax.: 03 90 24 46 86
>