Hello. I'm a Python newbie having problems trying to install galaxy on a Mac (PPC) running OSX 10.5.8 and Python 2.5.1.
Do I need to upgrade my Python or OSX version?
If not, below are the gory details for anyone who wants to help.
Arlin ----------------------------- gory details (narrative description followed by transcript) ---------------------
I've been through this several times and loaded various packages manually, and it all seems to come down to numpy 1.3.0 and bx-python 0.5.0. I installed more recent versions of these myself (numpy 1.4.1 and bx-python 0.6.0), and verified that they were installed correctly, but Galaxy seems to want specific versions that are not the current versions. I found a binary of numpy 1.3.0 but the installer would not let me install it on the grounds that it requires "System Python 2.5", which is confusing because thats what I thought I had. I haven't found bx-python 0.5.0 anywhere though I suppose I could just build an old release from the source repository.
camel12:dev arlin$ uname -a Darwin camel12.umbi.umd.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC Power Macintosh
camel12:dev arlin$ python --version Python 2.5.1
camel12:dev arlin$ hg clone http://bitbucket.org/galaxy/galaxy-dist (works fine)
camel12:dev arlin$ cd galaxy-dist/
camel12:galaxy-dist arlin$ sudo sh setup.sh . . . (lots of messages) Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.5.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 31, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/arlin/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 284, in resolve egg.resolve() File "/Users/arlin/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 172, in resolve r = pkg_resources .working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Library/Python/2.5/site-packages/distribute-0.6.10-py2.5.egg/ pkg_resources.py", line 565, in resolve ) pkg_resources.DistributionNotFound: bx-python==0.5.0-dev-f74aec067563
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------- Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org
Arlin Stoltzfus wrote:
Hello. I'm a Python newbie having problems trying to install galaxy on a Mac (PPC) running OSX 10.5.8 and Python 2.5.1.
Do I need to upgrade my Python or OSX version?
If not, below are the gory details for anyone who wants to help.
Hi Arlin,
Sorry for the late reply. It looks like your Python is not the system version (as evidenced by the path '/Library' as opposed to '/System/Library'), although it may be the python.org version, which is also supported.
Arlin ----------------------------- gory details (narrative description followed by transcript) ---------------------
I've been through this several times and loaded various packages manually, and it all seems to come down to numpy 1.3.0 and bx-python 0.5.0. I installed more recent versions of these myself (numpy 1.4.1 and bx-python 0.6.0), and verified that they were installed correctly, but Galaxy seems to want specific versions that are not the current versions. I found a binary of numpy 1.3.0 but the installer would not let me install it on the grounds that it requires "System Python 2.5", which is confusing because thats what I thought I had. I haven't found bx-python 0.5.0 anywhere though I suppose I could just build an old release from the source repository.
camel12:dev arlin$ uname -a Darwin camel12.umbi.umd.edu 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:57:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_PPC Power Macintosh
camel12:dev arlin$ python --version Python 2.5.1
camel12:dev arlin$ hg clone http://bitbucket.org/galaxy/galaxy-dist (works fine)
camel12:dev arlin$ cd galaxy-dist/
camel12:galaxy-dist arlin$ sudo sh setup.sh
!!
Galaxy should not be run as root, nor should the setup.
. . . (lots of messages) Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.5.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 31, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/arlin/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 284, in resolve egg.resolve() File "/Users/arlin/dev/galaxy-dist/lib/galaxy/eggs/__init__.py", line 172, in resolve r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Library/Python/2.5/site-packages/distribute-0.6.10-py2.5.egg/pkg_resources.py", line 565, in resolve ) pkg_resources.DistributionNotFound: bx-python==0.5.0-dev-f74aec067563
It looks like there may be conflicts with existing things in /Library/Python/2.5/site-packages, if there's a lot in there.
The safest thing to do here is to set up a virtualenv:
% wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py % python virtualenv.py galaxy_env --no-site-packages % ./galaxy_env/bin/activate % cd galaxy_dist % sh run.sh
And see if that solves it. If not, please let us know.
--nate
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Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org
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Arlin Stoltzfus -
Nate Coraor