[Pipet Devel] piper 0.0.0 suggestions

[J.W. Bizzaro]

I tried installing piper-0.0.0 as root, but running it as jeff, I get the
following errors:

-----------------------------------------------------------
jeff at dexter:loci> piper
Traceback (innermost last):
  File "/usr/bin/piper", line 24, in ?
    os.chmod("runpiper.py", 0755)
OSError: [Errno 1] Operation not permitted: 'runpiper.py'
-----------------------------------------------------------

The error is obviously because the root owns the file and jeff can't change
the mode.  Looking up the command, it seems chmod is run if permission denied
returned.  Here's why:

-rw-r--r--   1 root     root         2815 Jun  1 00:35 runpiper.py

Could/should chmod 0755 be run in the install script?

I have the same problem with...

    uil/pied/locignome.py
    dl/startdl.py
    'temp'  (wherever that goes)

You may also want to change this:

/usr/piper/uil/pied/modules/middlecommunicate.py lines 47-50:
-----------------------------------------------
			except socket.error:
				if (middle_started == 0):
					middle_started = 1
					os.system("./loci -g=off &")
-----------------------------------------------
                                                   ^^^^^^^^^^^^
                                                 command not found

A couple more things:

When I run...

  ./config --prefix=/usr

the usual...

    /usr/lib
    /usr/bin

get populated, and that's fine, but I also end up with...

    /usr/piper

which I'd rather not have.  Running RedHat Linux, I would put Piper's home dir
in...

    /usr/opt/piper   or   /usr/home/piper

My question is: Can we allow 2 locales to be defined on config?

Also, for the sake of updating Piper (when that time comes), would it be
better to specify the version number in the path, like...

    /usr/opt/piper-0.0.0

?   So that we don't mix the new with the old.

BTW Brad, I am utterly amazed by how much you've done to put this package
together.  And such a great job!  The install instructions are better than
I've seen for most applications, especially omniORB (ick).  I need to get off
my arse and make a better UI to go along with it.

Cheers.
Jeff
-- 
                      +----------------------------------+
                      |           J.W. Bizzaro           |
                      |                                  |
                      | http://bioinformatics.org/~jeff/ |
                      |                                  |
                      |        BIOINFORMATICS.ORG        |
                      |           The Open Lab           |
                      |                                  |
                      |    http://bioinformatics.org/    |
                      +----------------------------------+