HowTo for compiling emboss under windows

[voltigeur at worldonline.ch]

Hello,

This the (small) HowTo I told you about.
Some remarks: 
- it's only for emboss, since it seems that people
are more interested in it than in jemboss. I'll also
write one for jemboss, though (soon).
- it's how I did it on my computer, there might be
differences and/or different ways of doing it.
- I don't think there are mistakes, but who knows.
- bug-fixes, remarks are wellcome



EMBOSS:

1) install cygwin (http://www.cygwin.com). That's surely possible to 
compile without it, but it's making everything easier. You'll have
to install the base part plus the devel/make and devel/gcc packages. 
Before installing, see the first line of 2).
Then you'll have a linux-like command-line with tools like gcc and
make. The paths are then made according to the place where you installed
cygwin (ex: c\cygwin becomes /).

2) cygwin (and EMBOSS, and other linux/unix programs) don't like empty
spaces in names. Be sure that you install everything in places without
empty spaces (avoid "C:\Program Files\"). But by default cygwin uses your
windows login (something like "FirstName LastName") to create the 
/home/user_folder. Find and edit the /etc/passwd file and rename 
"FirstName LastName" into "FirstName_LastName" (or whatever else).

3) quit and restart the cygwin bash (you'll start in your "FirstName_LastName"
directory, you can delete "FirstName LastName"), download the EMBOSS 
package and cd to the place where you uncompressed it. Follow the usual

procedure:
./configure --without-x CFLAGS=-s
make
make install
 
--without-x because at one point the X11 library is required (even if 
useless) and without this flag the compilation would stop.
CFLAGS=-s to make the binaries smaller.

4) you can now use the EMBOSS programs from the cygwin bash like you
usually do from linux (but have a look at 5) and 6) before).

5) text files are different between windows and linux. If you save 
(for ex.) emboss.default from, say, wordpad, EMBOSS programs parsing
this file won't be able to pass the first line and they will crash.
To overcome this, use notepad instead (or save in a format you know
that it won't be a problem), or convert the file to linux
format (various tools are available on internet, it's a common problem).

6) EMBOSS has then been built with cygwin. To use it from a ms-dos cmd
instead of the cygwin bash the cygwin1.dll has to be in your windows
PATH (ex: C:\windows\system32).

good luck,

Olivier Martin