On Sep 2, 2011, at 1:16 PM, Nate Coraor wrote:

We haven't yet gotten our dependencies up to speed on Lion. Could you grab a copy of Python from python.org and use this? It'll install under /Library/Frameworks/Python.framework, just add the correct bin/ directory to the front of your $PATH and start Galaxy as normal.

i'm assuming this is similar? https://bitbucket.org/galaxy/galaxy-central/issue/616/bad-eggs-for-106

Thanks for the information, Nate. I installed Python as you described, and the error I get now is pasted below. I appreciate your help. Jeff [~/galaxy-dist] myuserid 03:06 PM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. [~/galaxy-dist] myuserid 03:06 PM > ________________________________________ From: Nate Coraor [nate@bx.psu.edu] Sent: Friday, September 02, 2011 1:16 PM To: Whyte, Jeffrey Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion) Whyte, Jeffrey wrote:

Hi,

I've been having trouble running a local instance of Galaxy on a Mac Pro after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed.

The error I see after running the startup script is pasted at the end of this message. Thanks in advance for any help or advice. jjw

Hi Jeffrey, We haven't yet gotten our dependencies up to speed on Lion. Could you grab a copy of Python from python.org and use this? It'll install under /Library/Frameworks/Python.framework, just add the correct bin/ directory to the front of your $PATH and start Galaxy as normal. Sorry for the inconvenience, --nate

-----

[~/galaxy-dist] myuserid 10:11 AM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. [~/galaxy-dist] myuserid 10:12 AM >

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Hi Nate, Thanks for the response. Here is the output: [~] myuserid 01:34 PM > python ./scripts/get_platforms.py /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file './scripts/get_platforms.py': [Errno 2] No such file or directory [~] myuserid 01:34 PM > Jeff ________________________________________ From: Nate Coraor [nate@bx.psu.edu] Sent: Tuesday, September 06, 2011 10:18 AM To: Whyte, Jeffrey Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion) Whyte, Jeffrey wrote:

Thanks for the information, Nate.

I installed Python as you described, and the error I get now is pasted below. I appreciate your help.

Jeff

[~/galaxy-dist] myuserid 03:06 PM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. [~/galaxy-dist] myuserid 03:06 PM >

Could you report back with the output of: % python ./scripts/get_platforms.py ? Thanks, --nate

________________________________________ From: Nate Coraor [nate@bx.psu.edu] Sent: Friday, September 02, 2011 1:16 PM To: Whyte, Jeffrey Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

Whyte, Jeffrey wrote:

...

Hi,

I've been having trouble running a local instance of Galaxy on a Mac Pro after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed.

The error I see after running the startup script is pasted at the end of this message. Thanks in advance for any help or advice. jjw

Hi Jeffrey,

We haven't yet gotten our dependencies up to speed on Lion. Could you grab a copy of Python from python.org and use this? It'll install under /Library/Frameworks/Python.framework, just add the correct bin/ directory to the front of your $PATH and start Galaxy as normal.

Sorry for the inconvenience, --nate

...

-----

[~/galaxy-dist] myuserid 10:11 AM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. [~/galaxy-dist] myuserid 10:12 AM >

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Whyte, Jeffrey wrote:

Nate,

For some reason, ~/galaxy-dist wasn't in my PATH. Here is the output when the script is run from the ~/galaxy-dist directory:

[~/galaxy-dist] myuserid 03:50 PM > python ./scripts/get_platforms.py macosx-10.6-intel-ucs2 [~/galaxy-dist] myuserid 03:50 PM >

Looks like it is set for Mac OS X 10.6 Snow Leopard instead of 10.7 Lion. (?)

This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform. I see there's now an Intel-only build for 10.6+, I'll work on this ASAP.

Thanks, Jeff

On Sep 6, 2011, at 10:18 AM, Nate Coraor wrote:

...

Whyte, Jeffrey wrote:

...

Thanks for the information, Nate.

I installed Python as you described, and the error I get now is pasted below. I appreciate your help.

Jeff

[~/galaxy-dist] myuserid 03:06 PM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. [~/galaxy-dist] myuserid 03:06 PM >

Could you report back with the output of:

% python ./scripts/get_platforms.py

?

Thanks, --nate

...

________________________________________ From: Nate Coraor [nate@bx.psu.edu] Sent: Friday, September 02, 2011 1:16 PM To: Whyte, Jeffrey Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

Whyte, Jeffrey wrote:

...

Hi,

I've been having trouble running a local instance of Galaxy on a Mac Pro after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed.

The error I see after running the startup script is pasted at the end of this message. Thanks in advance for any help or advice. jjw

Hi Jeffrey,

We haven't yet gotten our dependencies up to speed on Lion. Could you grab a copy of Python from python.org and use this? It'll install under /Library/Frameworks/Python.framework, just add the correct bin/ directory to the front of your $PATH and start Galaxy as normal.

Sorry for the inconvenience, --nate

...

-----

[~/galaxy-dist] myuserid 10:11 AM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. [~/galaxy-dist] myuserid 10:12 AM >

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Trevor Wennblom wrote:

On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote:

...

This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform.

I see there's now an Intel-only build for 10.6+, I'll work on this ASAP.

if it helps, here are details from 10.7

% /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python -V Python 2.7.1 % file /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7: Mach-O fat file with 2 architectures % /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python scripts/get_platforms.py macosx-10.7-intel-ucs2

Yeah, this will be a new egg. I'm getting access to a Lion machine shortly and can build for this.

% /usr/local/bin/python -V Python 2.7.2 % file /usr/local/Cellar/python/2.7.2/bin/python2.7 /usr/local/Cellar/python/2.7.2/bin/python2.7: Mach-O 64-bit executable % /usr/local/bin/python scripts/get_platforms.py macosx-10.4-x86_64-ucs2

Only one architecture. This one you'll be on your own building eggs for. You should be able to with scramble.py, though.

% brew --config HOMEBREW_VERSION: 0.8 HEAD: 8ba7bf8a53dd750943552458daf824e8c424db23 HOMEBREW_PREFIX: /usr/local HOMEBREW_CELLAR: /usr/local/Cellar HOMEBREW_REPOSITORY: /usr/local HOMEBREW_LIBRARY_PATH: /usr/local/Library/Homebrew Hardware: dual-core 64-bit penryn OS X: 10.7.1 Kernel Architecture: x86_64 Ruby: 1.8.7-249 /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby Xcode: 4.1 GCC-4.0: N/A GCC-4.2: build 5666 LLVM: build 2335 MacPorts or Fink? false X11 installed? true

% uname -rv 11.1.0 Darwin Kernel Version 11.1.0: Tue Jul 26 16:07:11 PDT 2011; root:xnu-1699.22.81~1/RELEASE_X86_64 % uname -p i386 % uname -m x86_64