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---------- Forwarded message ----------
From: James Casbon <casbon(a)gmail.com>
Date: 2008/9/12
Subject: Re: [galaxy-user] Install problems on OS X with python from macports
To: Nate Coraor <nate(a)bx.psu.edu>
2008/9/12 Nate Coraor <nate(a)bx.psu.edu>:
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:
It's the egg downloader doing md5s on the files. I think there are
two ways hashlib can work, and I think the macports way is to use the
_hashlib c implementation, which goes missing from the path. This is
probably because MacPorts choose to split out hashlib from the base
install.
-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.
I can get hashlib from the interactive shell. Is there a way to get a
shell with the galaxy environment?
Here is the traceback. If you read hashlib, it tries to import
_hashlib and if that fails and so it tries to get _md5. The MacPorts
python should have _hashlib but not _md5 (as below). _hashlib cannot
be found with the path for some reason.
Traceback (most recent call last):
File "scramble.py", line 11, in <module>
use_setuptools( download_delay=8, to_dir=scramble_lib )
File
"/Users/james/Src/galaxy_dist/scripts/scramble/build/py2.5-macosx-10.3-i386-ucs2/Cheetah/ez_setup.py",
line 91, in use_setuptools
return do_download()
File
"/Users/james/Src/galaxy_dist/scripts/scramble/build/py2.5-macosx-10.3-i386-ucs2/Cheetah/ez_setup.py",
line 85, in do_download
egg = download_setuptools(version, download_base, to_dir, download_delay)
File
"/Users/james/Src/galaxy_dist/scripts/scramble/build/py2.5-macosx-10.3-i386-ucs2/Cheetah/ez_setup.py",
line 120, in download_setuptools
import urllib2, shutil
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/urllib2.py",
line 91, in <module>
import hashlib
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/hashlib.py",
line 133, in <module>
md5 = __get_builtin_constructor('md5')
File
"/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/hashlib.py",
line 60, in __get_builtin_constructor
import _md5
ImportError: No module named _md5
> 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.).
OK I will try these flags out and see what happens.
Thanks for the quick reply,
James
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