[BioPython] installation help

[Jeffrey Chang]

On Mon, Jan 13, 2003 at 02:30:29PM -0700, Sevinsky Joel wrote:
> Andrew,
> 
> So I am rather new to this but the following seems pretty strange.  I
> looked at importing Martel and this is what I got:
> 
> [sevinsky@atreides sevinsky]$ python
> Python 2.2.1 (#1, Sep  9 2002, 09:26:21)
> [GCC 3.2 (Mandrake Linux 9.0 3.2-1mdk)] on linux-i386
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import Martel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/reportlab/__init__.py", line 6, in ?
>     __doc__="""The Reportlab PDF generation library."""
>   File "Martel/Expression.py", line 33, in ?
>   File "Martel/Parser.py", line 33, in ?
> ImportError: No module named TextTools
> >>> import Bio
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/biopython-1.10/Bio/__init__.py", line 65, in ?
>     _load_registries()
>   File "/usr/local/biopython-1.10/Bio/__init__.py", line 57, in
> _load_registries
>     module = __import__("Bio.config.%s" % module, {}, {},
> ["Bio","config"])
>   File "/usr/local/biopython-1.10/Bio/config/DBRegistry.py", line 35, in ?
>     from Bio import StdHandler
>   File "/usr/local/biopython-1.10/Bio/StdHandler.py", line 5, in ?
>     from Bio import Std, Decode
>   File "/usr/local/biopython-1.10/Bio/Std.py", line 4, in ?
>     Group = Martel.Group
> AttributeError: 'module' object has no attribute 'Group'

Having reportlab in the tracelab is very strange.  Are you sure you
need it?  If you don't know, then that means you probably don't.  Try
getting rid of that first.  Also, it seems to be installed at
/usr/local.  Are you installing modules there instead of
/usr/local/lib/python-2.2/site-packages/ ?  Looking at the PYTHONPATH
you posted earlier, it looks like the answer is YES.  The first thing
I would try is to get rid of those (don't install python libraries in
/usr/local/) and reinstall everything in python's path.

Jeff