[Pipet Devel] New directory structure

[Brad Chapman]

Hello everybody;
    I just finished getting piper building/installing in the way that 
we discussed on the list, so I was hoping people might be able to take 
a look at it and see what they think. You can grab the tarball from my 
spiffy bioinformatics.org site (courtesy o' Gary): 
http://alpha.bioinformatics.org/bradstuff/index.html. I would be 
really appreciative if you could try installing it and let me know 
what you think of the installation locations and directory structure.
    I'm using autoconf/automake for the build/install process. Right 
now things are really simple and you shouldn't need any patches to 
autoconf at all. I'm going to work on understanding better the m4s 
that are available for python and work on getting the .py files 
byte-compiled before I install them (the way it is supposed to be done 
:-).
    I'll update the install instructions in the distribution 
tonight/tommorrow, but here is the simple overview:

1. To just install it, you should just need to type ./configure && 
make && make install, just like with any autoconfed build. 
    Right now configure takes the following options:
    1.--prefix=/the/location/you/want/to/put/piper (deafaults as 
/usr/local)
    2.--with-peep-ui or --without-peep-ui (the default is with if you 
don't put
    anything)
    3. --with-pied-ui or --without-pied-ui (like peep)

2. To build it using autoconf, you should be able to just run:

./autogen.sh <the arguments to pass to configure>

This script will do all the aclocal, automake, autoconf stuff for you 
(thanks to the Overflow guys for this fine script).

    Piper installs into the following directories under the specified 
$prefix:

    bin -> The executables for piper ('piper' and 'piperpass')
    piper -> All of the stuff that makes up piper
    share/pixmaps/piper -> The pixmaps for the gnome ui (pied)

I've made an attempt to help separate the different sections of Piper 
so that we can break away from being all python. The dl, peep and pied 
are all "stand-alone" so that they have their own directories and 
configure scripts. The main script that runs 'piper' (name changed 
to runpiper.py) no longer imports python modules, but instead just 
runs scripts provided by the different modules. Right now pied and the 
dl have scripts that can be run, Deanne'll need to get one going for 
peep once there is something there.
    I think that's it :-) Thanks for reading all the way down. I'll 
work on fixing the install documentation and getting a snazzier 
byte-compiled installation, but I'd really like to get people's 
opinions on this structure and install before we stick it in cvs. 
Thanks much!

Brad