EMBOSS under Mac OS-X ?

Don Gilbert gilbertd at bio.indiana.edu
Mon May 14 03:15:43 EST 2001


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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