Dear Nate,

I've been doing exactly that. What's driving me crazy is that every second compile (bx_python, numpy, pysam) runs into a Cygwin DLL remap failure that cannot be resolved with /bin/rebaseall. So any advice on how to get rid of that would be great. Right now it's failing in the bx_python build on lapack_lite.dll or mtrand.dll (or randomly on a bunch of other cyg* dlls).

Thanks,
Oren

Oren,

In addition to everything Dannon said, I'll add that the specific
problem here is that we don't pre-build Python eggs for Cygwin.  If
you're still trying to do this, I'd suggest running
scripts/fetch_eggs.py once to grab all platform-agnostic eggs, and then
scripts/scramble.py to try to build the rest.  Good luck!

--nate


On Oct 12, 2011, at 02:50 PM, Oren Livne<li...@uchicago.edu>  wrote:

Dear All,

There are related posts but it is unclear from them how to resolve
the following. I'm trying to start a Galaxy server on Cygwin and it
fails when trying to fetch an egg relying on NumPy. Could you kindly
advise how to resolve the error?

This uses the Cygwin python 2.6.5. I tried to point Cygwin to the
Windows python (2.7.2 in my case) but that was even worse, the Mako
egg threw a KeyError: 'Mako' exception up front.

Thank you so much,
Oren

--------
$ python --version
Python 2.6.5

oren@oren-PC /cygdrive/c/web/galaxy-central
$ sh run.sh --reload
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.g2bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-01-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py26.egg
Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg
Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 30, in<module>
c.resolve() # Only fetch eggs required by the config
File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py",
line 345, i
n resolve
egg.resolve()
File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py",
line 195, i
n resolve
return self.version_conflict( e.args[0], e.args[1] )
File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py",
line 226, i
n version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
env, egg.
fetch )
File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line
565, in resol
ve
raise DistributionNotFound(req) # XXX put more info here
pkg_resources.DistributionNotFound: numpy==1.6.0
Fetch failed.

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