Re: [galaxy-dev] homebrew python
Thanks! I was able to side-step most of the fetch failures by copying the eggs by hand into the eggs folder (copying them from an old galaxy-dist) or installing them using pip. I have not applied the patch to test it, sorry. I'll try it when I update. My troubles started from trying to install MACS2 on a galaxy-dist of OSX. It has several dependencies. Looking back, it appears that the problem was that the OSX system python did NOT have the readlines support compiled in. Thus, the homebrew version python I configured with readlines. Only after the painful workaround, did I notice that there was a readlines library in the toolshed, but I'm not sure if that would have fixed the problem or not. On Fri, Mar 28, 2014 at 1:24 PM, Nate Coraor wrote: > Hi Joshua, > > You may be able to trick Galaxy into using existing versions of OS X eggs, > they are built for both 32 and 64-bit Intel, but should work fine with a > single-arch build. If the attached patch works, let me know and I'll commit > it. > > If you'd rather not mess with the Galaxy source, you should be able to > build the missing eggs using `python ./scripts/scramble.py -e > `. Usually, the fetch_eggs.py script will inform you of > this - is it not doing so in your case? > > --nate > > > On Mon, Mar 24, 2014 at 9:54 PM, Joshua Udall wrote: > >> For various reasons, I installed a Homebrew of python instead of the >> system version on OSX 10.9.2. >> >> Now, when galaxy initializes, it isn't looking in the right location for >> eggs (or they aren't placed in the right spot on my system). I was able to >> manually install several of the eggs and the galaxy startup would move to >> the next egg until here. >> >> Some eggs are out of date, attempting to fetch... >> Warning: MarkupSafe (a dependent egg of WebHelpers) cannot be fetched >> Traceback (most recent call last): >> File "./scripts/fetch_eggs.py", line 37, in >> c.resolve() # Only fetch eggs required by the config >> File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 345, >> in resolve >> egg.resolve() >> File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195, >> in resolve >> return self.version_conflict( e.args[0], e.args[1] ) >> File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226, >> in version_conflict >> r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), >> env, egg.fetch ) >> File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, >> in resolve >> The `plugin_env` should be an ``Environment`` instance that contains >> pkg_resources.DistributionNotFound: numpy==1.6.0 >> Fetch failed. >> >> >> I know numpy, WebHelpers, MarkupSafe are installed and they are current >> (maybe too current?) ... what would be a good way to resolve the conflict? >> >> The manual download below fails on a dozen packages or so. >> >> sudo python ./scripts/make_egg_packager.py py2.7-macosx-10.9-x86_64-ucs2 >> Using Python interpreter at >> /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python, >> Version 2.7.6 (default, Mar 24 2014, 14:39:40) >> [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)] >> This platform is 'py2.7-macosx-10.9-x86_64-ucs2' >> Override with: >> make_egg_packager.py >> Completed packager is 'egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py'. >> To >> fetch eggs, please copy this file to a system with internet access and run >> with: >> python egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py >> >> -- >> Joshua Udall >> Assistant Professor >> 295 WIDB >> Plant and Wildlife Science Dept. >> Brigham Young University >> Provo, UT 84602 >> 801-422-9307 >> Fax: 801-422-0008 >> USA >> >> ___ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > -- Joshua Udall (295 WIDB) Brigham Young University 685 E. University Parkway Plant and Wildlife Science Depart. Provo, UT 84602 Office: 801-422-9307 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] homebrew python
Hi Joshua, You may be able to trick Galaxy into using existing versions of OS X eggs, they are built for both 32 and 64-bit Intel, but should work fine with a single-arch build. If the attached patch works, let me know and I'll commit it. If you'd rather not mess with the Galaxy source, you should be able to build the missing eggs using `python ./scripts/scramble.py -e `. Usually, the fetch_eggs.py script will inform you of this - is it not doing so in your case? --nate On Mon, Mar 24, 2014 at 9:54 PM, Joshua Udall wrote: > For various reasons, I installed a Homebrew of python instead of the > system version on OSX 10.9.2. > > Now, when galaxy initializes, it isn't looking in the right location for > eggs (or they aren't placed in the right spot on my system). I was able to > manually install several of the eggs and the galaxy startup would move to > the next egg until here. > > Some eggs are out of date, attempting to fetch... > Warning: MarkupSafe (a dependent egg of WebHelpers) cannot be fetched > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 37, in > c.resolve() # Only fetch eggs required by the config > File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 345, > in resolve > egg.resolve() > File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195, > in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226, > in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), > env, egg.fetch ) > File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, in > resolve > The `plugin_env` should be an ``Environment`` instance that contains > pkg_resources.DistributionNotFound: numpy==1.6.0 > Fetch failed. > > > I know numpy, WebHelpers, MarkupSafe are installed and they are current > (maybe too current?) ... what would be a good way to resolve the conflict? > > The manual download below fails on a dozen packages or so. > > sudo python ./scripts/make_egg_packager.py py2.7-macosx-10.9-x86_64-ucs2 > Using Python interpreter at > /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python, > Version 2.7.6 (default, Mar 24 2014, 14:39:40) > [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)] > This platform is 'py2.7-macosx-10.9-x86_64-ucs2' > Override with: > make_egg_packager.py > Completed packager is 'egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py'. To > fetch eggs, please copy this file to a system with internet access and run > with: > python egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py > > -- > Joshua Udall > Assistant Professor > 295 WIDB > Plant and Wildlife Science Dept. > Brigham Young University > Provo, UT 84602 > 801-422-9307 > Fax: 801-422-0008 > USA > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > osx_intel_platform.patch Description: Binary data ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] homebrew python
For various reasons, I installed a Homebrew of python instead of the system version on OSX 10.9.2. Now, when galaxy initializes, it isn't looking in the right location for eggs (or they aren't placed in the right spot on my system). I was able to manually install several of the eggs and the galaxy startup would move to the next egg until here. Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in c.resolve() # Only fetch eggs required by the config File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, in resolve The `plugin_env` should be an ``Environment`` instance that contains pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. I know numpy, WebHelpers, MarkupSafe are installed and they are current (maybe too current?) ... what would be a good way to resolve the conflict? The manual download below fails on a dozen packages or so. sudo python ./scripts/make_egg_packager.py py2.7-macosx-10.9-x86_64-ucs2 Using Python interpreter at /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python, Version 2.7.6 (default, Mar 24 2014, 14:39:40) [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)] This platform is 'py2.7-macosx-10.9-x86_64-ucs2' Override with: make_egg_packager.py Completed packager is 'egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py'. To fetch eggs, please copy this file to a system with internet access and run with: python egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
