homebrew python

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homebrew python

bnapus
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Some eggs are out of date, attempting to fetch...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 <module>
    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 <forced-platform>
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

___________________________________________________________
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Re: homebrew python

Nate Coraor (nate@bx.psu.edu)
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 <egg_package_name>`. 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 <[hidden email]> 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 <module>
    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 <forced-platform>
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
<a href="tel:801-422-9307" value="+18014229307" target="_blank">801-422-9307
Fax: <a href="tel:801-422-0008" value="+18014220008" target="_blank">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/


___________________________________________________________
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 (3K) Download Attachment
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Re: homebrew python

Joshua Udall
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 <[hidden email]> 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 <egg_package_name>`. 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 <[hidden email]> 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 <module>
    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 <forced-platform>
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
<a href="tel:801-422-9307" value="+18014229307" target="_blank">801-422-9307
Fax: <a href="tel:801-422-0008" value="+18014220008" target="_blank">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/