Oren Livne wrote: > 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).
Hi Oren, I've used Cygwin once, so I'm afraid I can't be of any help here. --nate > > 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Some eggs are out of date, attempting to fetch...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. > >> > >>___________________________________________________________ > >>The Galaxy User list should be used for the discussion of > >>Galaxy analysis and other features on the public server > >>at usegalaxy.org. Please keep all replies on the list by > >>using "reply all" in your mail client. For discussion of > >>local Galaxy instances and the Galaxy source code, please > >>use the Galaxy Development list: > >> > >>http://lists.bx.psu.edu/listinfo/galaxy-dev > >> > >>To manage your subscriptions to this and other Galaxy lists, > >>please use the interface at: > >> > >>http://lists.bx.psu.edu/ > >>___________________________________________________________ > >>Please keep all replies on the list by using "reply all" > >>in your mail client. To manage your subscriptions to this > >>and other Galaxy lists, please use the interface at: > >> > >> http://lists.bx.psu.edu/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
