James Casbon wrote:
I'm trying to do a local install of Galaxy. My python version is
MacPorts. I realize that you recommend using MacPython, but since all
the dev environment I have uses MacPorts, I thought I'd give it a go.
BTW, it does work with the shipped python 2.5 with OS X.
Thanks! Good to know.
The problem I have is that the egg downloading part (scramble.py,
etc.) seems to monkey with the pythonpath such that _hashlib cannot be
imported. I tried to track what happens, but it is not obvious where
and why the path is being changed.
I'm not sure what's trying to import _hashlib... but what's stranger is
that it should be part of the base python install, and nothing we do
affects the base install. We do start Galaxy with these flags:
-E Ignore environment variables like PYTHONPATH and PYTHONHOME
that modify the behavior of the interpreter.
-S Disable the import of the module site and the site-dependent
manipulations of sys.path that it entails.
This is so we can limit conflicts between our provided dependencies, and
any you may have installed locally.
If you start the interactive interpreter, are you able to import
_hashlib? How about with -E and/or -S? Any output you can provide from
where it fails (I assume in scramble.py?) would be helpful.
How can I safely add something to galaxy's pythonpath and ensure
Remove -E from run.sh, if necessary, but this may cause other problems.
Tools do run without these flags so they can find other site-installed
dependencies (such as numpy, etc.).