Hi James, James Casbon wrote:

I'm trying to do a local install of Galaxy. My python version is from 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 it is not removed?

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.). --nate