Hi Jake, Jacob Biesinger wrote:
A number of eggs were missing for my platform (Intel Mac OS 10.4, python 2.5) and I had to scramble a number of eggs. These included the following: pycrypto lzo_python Cheetah pysqlite bx_python
Python 2.5 on OS X Intel is a supported platform, but it looks like your Python isn't Universal (it doesn't support dual architectures). Which version of OS X are you using, and which Python (MacPorts)? For 10.4, MacPython is recommended: http://www.macpython.org/packages/ For 10.5, the system Python should work, but this has not been tested. If you stick with your current single-arch python, that's fine, but you won't have the benefit of pre-scrambled eggs (ours are for universal python only).
Scrambling my own eggs worked fine except for with pysqlite. I grabbed version 3.5.4 of sqlite3.c file and built a static pysqlite egg file.
Can you provide the error you got from scramble? pysqlite scrambles out of the box for me on an Intel Mac, but I'm not using the same python as you.
When I first ran run.sh, the web server loaded just fine. But on attempting to upload a file, I got the following dump, which says to me that galaxy is using a local install of Cheetah rather than the egg that I scrambled:
File '/opt/local/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-macosx-10.3-i386.egg/Cheetah/Template.py', line 777 in compile raise e IndentationError: expected an indented block (_Users_wjb_Projects_galaxy_templates_tool_form_tmpl.py, line 226)
Our templates aren't currently Cheetah 2.x compatible. This is a strange problem, though, as paths in your $PYTHONPATH (which is set by the init scripts) should be placed at the beginning of sys.path, thus, our eggs should override your local modules. I have seen this happen with a few other people as well, but I can't duplicate it myself.
File "/Users/wjb/Projects/galaxy/eggs/py2.5-macosx-10.3-i386-ucs2/Cheetah-1.0-py2.5-macosx-10.3-i386.egg/Cheetah/NameMapper.py", line 146 SyntaxError: from __future__ imports must occur at the beginning of the file
I have a fix for this which I've just committed in rev 2514. Please update your copy of Galaxy and scramble Cheetah again. --nate