Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas? Thanks! Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Paul Tanger wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the fact that I have EPD python, not the generic python that was preinstalled? Any ideas?
Thanks!
Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Hi Paul, Can you give it a try with the system Python and see if you get the same result? All you need to do is put: /System/Library/Frameworks/Python.framework/Versions/2.6/bin At the head of your $PATH. Thanks, --nate
___________________________________________________________ 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:
Yes it works with the default python install. Any way I can get it working with EPD python? On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
2.6 (EPD version 6.1-1)? I get this error which I suspect is related to
fact that I have EPD python, not the generic python that was
Paul Tanger wrote: python the preinstalled?
Any ideas?
Thanks!
Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get the same result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
___________________________________________________________ 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:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here. One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of: galaxy-dist/lib/galaxy/eggs/__init__.py After the import of pkg_resources and see which version it's using. --nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
2.6 (EPD version 6.1-1)? I get this error which I suspect is related to
fact that I have EPD python, not the generic python that was
Paul Tanger wrote: python the preinstalled?
Any ideas?
Thanks!
Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get the same result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
___________________________________________________________ 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:
It is free for academic use. I'll try what you suggested below - thanks! On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
Paul Tanger wrote: python
2.6 (EPD version 6.1-1)? I get this error which I suspect is related
fact that I have EPD python, not the generic python that was
the preinstalled?
Any ideas?
Thanks!
Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
to line line
184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get the same result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
___________________________________________________________ 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:
sys path is: ['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib'] pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'> On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <paul.tanger@colostate.edu>wrote:
It is free for academic use. I'll try what you suggested below - thanks!
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD
2.6 (EPD version 6.1-1)? I get this error which I suspect is related to
fact that I have EPD python, not the generic python that was
python the preinstalled?
Any ideas?
Thanks!
Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
(enthought) line line
184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get the same result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
___________________________________________________________ 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:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL', '/Users/paultanger/galaxy-dist/lib']
Hi Paul, If you replace: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) With: lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib ) In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect? --nate
pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <paul.tanger@colostate.edu>wrote:
It is free for academic use. I'll try what you suggested below - thanks!
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Has anyone gotten galaxy installed on a mac 10.5 with EPD
2.6 (EPD version 6.1-1)? I get this error which I suspect is related to
fact that I have EPD python, not the generic python that was
python the preinstalled?
Any ideas?
Thanks!
Some eggs are out of date, attempting to fetch... 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
345, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
(enthought) line line
184, in resolve if e.args[0].project_name != self.distribution.project_name: AttributeError: 'str' object has no attribute 'project_name' Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get the same result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
___________________________________________________________ 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:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is: pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch... pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
pkg_resources is: <module 'pkg_resources' from
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <paul.tanger@colostate.edu wrote:
It is free for academic use. I'll try what you suggested below -
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we
can
do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu>
wrote:
Paul Tanger wrote: > Has anyone gotten galaxy installed on a mac 10.5 with EPD
python > 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the > fact that I have EPD python, not the generic python that was preinstalled? > Any ideas? > > Thanks! > > Some eggs are out of date, attempting to fetch... > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> 345, in resolve > egg.resolve() > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
(enthought) line line
> 184, in resolve > if e.args[0].project_name != self.distribution.project_name: > AttributeError: 'str' object has no attribute 'project_name' > Fetch failed.
Hi Paul,
Can you give it a try with the system Python and see if you get
thanks! the
same
result? All you need to do is put:
/System/Library/Frameworks/Python.framework/Versions/2.6/bin
At the head of your $PATH.
Thanks, --nate
> ___________________________________________________________ > 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/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177 paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is:
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
It could be a conflict with the existing version, try: python -ES ./scripts/fetch_eggs.py --nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
pkg_resources is: <module 'pkg_resources' from
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <paul.tanger@colostate.edu wrote:
It is free for academic use. I'll try what you suggested below -
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working with EPD python?
I've never worked with EPD and since it's not free it's unlikely we
can
do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu>
wrote:
> Paul Tanger wrote: > > Has anyone gotten galaxy installed on a mac 10.5 with EPD
> python > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to > the > > fact that I have EPD python, not the generic python that was > preinstalled? > > Any ideas? > > > > Thanks! > > > > Some eggs are out of date, attempting to fetch... > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> > 345, in resolve > > egg.resolve() > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
(enthought) line line
> > 184, in resolve > > if e.args[0].project_name != self.distribution.project_name: > > AttributeError: 'str' object has no attribute 'project_name' > > Fetch failed. > > Hi Paul, > > Can you give it a try with the system Python and see if you get
thanks! the
same
> result? All you need to do is put: > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin > > At the head of your $PATH. > > Thanks, > --nate > > > ___________________________________________________________ > > 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/ > >
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
That worked, for everything but pysam. I also tried to install it directly: pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Some eggs are out of date, attempting to fetch... pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> 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. On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is:
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
pkg_resources is: <module 'pkg_resources' from
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', paul.tanger@colostate.edu
wrote:
It is free for academic use. I'll try what you suggested below - thanks!
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote: > Yes it works with the default python install. Any way I can get it working > with EPD python?
I've never worked with EPD and since it's not free it's unlikely we can do much debugging on it here. It would appear that they bundle a version of pkg_resources which changes the DistributionNotFound class, but it's hard to know exactly what's going on here.
One thing that might shed a bit of light on it would be to print sys.path and pkg_resources at the top of:
galaxy-dist/lib/galaxy/eggs/__init__.py
After the import of pkg_resources and see which version it's using.
--nate
> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote: > > > Paul Tanger wrote: > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) > > python > > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to > > the > > > fact that I have EPD python, not the generic python that was > > preinstalled? > > > Any ideas? > > > > > > Thanks! > > > > > > Some eggs are out of date, attempting to fetch... > > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line > > > 345, in resolve > > > egg.resolve() > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line > > > 184, in resolve > > > if e.args[0].project_name != self.distribution.project_name: > > > AttributeError: 'str' object has no attribute 'project_name' > > > Fetch failed. > > > > Hi Paul, > > > > Can you give it a try with the system Python and see if you get the same > > result? All you need to do is put: > > > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin > > > > At the head of your $PATH. > > > > Thanks, > > --nate > > > > > ___________________________________________________________ > > > 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/ > > > >
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177 paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
Paul Tanger wrote:
That worked, for everything but pysam. I also tried to install it directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> 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.
What platform do you get from: python ./scripts/get_platforms.py ? Note that this needs to have the path changed from append to insert as in the previous scripts. Thanks, --nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is:
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
pkg_resources is: <module 'pkg_resources' from
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin', paul.tanger@colostate.edu
wrote:
It is free for academic use. I'll try what you suggested below - thanks!
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote:
> Paul Tanger wrote: > > Yes it works with the default python install. Any way I can get it > working > > with EPD python? > > I've never worked with EPD and since it's not free it's unlikely we can > do much debugging on it here. It would appear that they bundle a > version of pkg_resources which changes the DistributionNotFound class, > but it's hard to know exactly what's going on here. > > One thing that might shed a bit of light on it would be to print > sys.path and pkg_resources at the top of: > > galaxy-dist/lib/galaxy/eggs/__init__.py > > After the import of pkg_resources and see which version it's using. > > --nate > > > > > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor <nate@bx.psu.edu> wrote: > > > > > Paul Tanger wrote: > > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD > (enthought) > > > python > > > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is > related to > > > the > > > > fact that I have EPD python, not the generic python that was > > > preinstalled? > > > > Any ideas? > > > > > > > > Thanks! > > > > > > > > Some eggs are out of date, attempting to fetch... > > > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > line > > > > 345, in resolve > > > > egg.resolve() > > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > line > > > > 184, in resolve > > > > if e.args[0].project_name != self.distribution.project_name: > > > > AttributeError: 'str' object has no attribute 'project_name' > > > > Fetch failed. > > > > > > Hi Paul, > > > > > > Can you give it a try with the system Python and see if you get the > same > > > result? All you need to do is put: > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin > > > > > > At the head of your $PATH. > > > > > > Thanks, > > > --nate > > > > > > > ___________________________________________________________ > > > > 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/ > > > > > > >
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2 On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor <nate@bx.psu.edu> wrote:
That worked, for everything but pysam. I also tried to install it
Paul Tanger wrote: directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> 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.
What platform do you get from:
python ./scripts/get_platforms.py
? Note that this needs to have the path changed from append to insert as in the previous scripts.
Thanks, --nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is:
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.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
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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts', '/Users/paultanger/python/scripts',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
'/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
pkg_resources is: <module 'pkg_resources' from
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger <
paul.tanger@colostate.edu
wrote:
> It is free for academic use. I'll try what you suggested below
thanks!
> > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote: > >> Paul Tanger wrote: >> > Yes it works with the default python install. Any way I can get it >> working >> > with EPD python? >> >> I've never worked with EPD and since it's not free it's unlikely we can >> do much debugging on it here. It would appear that they bundle a >> version of pkg_resources which changes the DistributionNotFound class, >> but it's hard to know exactly what's going on here. >> >> One thing that might shed a bit of light on it would be to
http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg line line line - print
>> sys.path and pkg_resources at the top of: >> >> galaxy-dist/lib/galaxy/eggs/__init__.py >> >> After the import of pkg_resources and see which version it's using. >> >> --nate >> >> > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor < nate@bx.psu.edu> wrote: >> > >> > > Paul Tanger wrote: >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD >> (enthought) >> > > python >> > > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is >> related to >> > > the >> > > > fact that I have EPD python, not the generic python that was >> > > preinstalled? >> > > > Any ideas? >> > > > >> > > > Thanks! >> > > > >> > > > Some eggs are out of date, attempting to fetch... >> > > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", >> line >> > > > 345, in resolve >> > > > egg.resolve() >> > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", >> line >> > > > 184, in resolve >> > > > if e.args[0].project_name != self.distribution.project_name: >> > > > AttributeError: 'str' object has no attribute 'project_name' >> > > > Fetch failed. >> > > >> > > Hi Paul, >> > > >> > > Can you give it a try with the system Python and see if you get the >> same >> > > result? All you need to do is put: >> > > >> > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin >> > > >> > > At the head of your $PATH. >> > > >> > > Thanks, >> > > --nate >> > > >> > > >
>> > > > 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/ >> > > >> > > >> > > >
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177 paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
Paul Tanger wrote:
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2
Okay, it looks like EPD python is only compiled for one platform. To use this, you'll need to scramble your own versions of the eggs which use C code. Could you try scrambling pysam as instructed below and see what the results are? You will have to do this for each egg that can't be downloaded. --nate
On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor <nate@bx.psu.edu> wrote:
That worked, for everything but pysam. I also tried to install it
Paul Tanger wrote: directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> 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.
What platform do you get from:
python ./scripts/get_platforms.py
? Note that this needs to have the path changed from append to insert as in the previous scripts.
Thanks, --nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is:
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.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
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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
Paul Tanger wrote: > sys path is: > > ['/Users/paultanger/galaxy-dist/scripts', > '/Users/paultanger/python/scripts', >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
>
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> '/Users/paultanger/galaxy-dist/lib']
Hi Paul,
If you replace:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib )
With:
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.insert( 0, lib )
In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an effect?
--nate
> > pkg_resources is: > <module 'pkg_resources' from >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger < paul.tanger@colostate.edu >wrote: > > > It is free for academic use. I'll try what you suggested below
thanks! > > > > > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor <nate@bx.psu.edu> wrote: > > > >> Paul Tanger wrote: > >> > Yes it works with the default python install. Any way I can get it > >> working > >> > with EPD python? > >> > >> I've never worked with EPD and since it's not free it's unlikely we can > >> do much debugging on it here. It would appear that they bundle a > >> version of pkg_resources which changes the DistributionNotFound class, > >> but it's hard to know exactly what's going on here. > >> > >> One thing that might shed a bit of light on it would be to
http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg line line line - print
> >> sys.path and pkg_resources at the top of: > >> > >> galaxy-dist/lib/galaxy/eggs/__init__.py > >> > >> After the import of pkg_resources and see which version it's using. > >> > >> --nate > >> > >> > > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor < nate@bx.psu.edu> wrote: > >> > > >> > > Paul Tanger wrote: > >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD > >> (enthought) > >> > > python > >> > > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is > >> related to > >> > > the > >> > > > fact that I have EPD python, not the generic python that was > >> > > preinstalled? > >> > > > Any ideas? > >> > > > > >> > > > Thanks! > >> > > > > >> > > > Some eggs are out of date, attempting to fetch... > >> > > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > >> line > >> > > > 345, in resolve > >> > > > egg.resolve() > >> > > > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > >> line > >> > > > 184, in resolve > >> > > > if e.args[0].project_name != self.distribution.project_name: > >> > > > AttributeError: 'str' object has no attribute 'project_name' > >> > > > Fetch failed. > >> > > > >> > > Hi Paul, > >> > > > >> > > Can you give it a try with the system Python and see if you get the > >> same > >> > > result? All you need to do is put: > >> > > > >> > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin > >> > > > >> > > At the head of your $PATH. > >> > > > >> > > Thanks, > >> > > --nate > >> > > > >> > > >
> >> > > > Please keep all replies on the list by using "reply all" > >> > > > in your mail client. To manage your subscriptions to this > >> > > > and other Galaxy lists, please use the interface at: > >> > > > > >> > > > http://lists.bx.psu.edu/ > >> > > > >> > > > >> > > > > > >
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
Yes I tried that but it didn't work. The entire output I pasted below in case you are interested. Thanks for your assistance so far, but I think I'm going to give up and just use ubuntu via virtualbox to run galaxy. paul-tangers-macbook-pro:galaxy-dist paultanger$ python scripts/scramble.py -e pysam pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'> pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'> fetch_one(): Using existing source, remove to download again: /Users/paultanger/galaxy-dist/scripts/scramble/archives/pysam-0.4.2_kanwei_b10f6e722e9a.tar.gz unpack_source(): Removing old build directory at: /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam unpack_source(): Unpacked to: /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam copy_build_script(): Using build script /Users/paultanger/galaxy-dist/scripts/scramble/scripts/generic.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam: /Library/Frameworks/Python.framework/Versions/6.1/Resources/Python.app/Contents/MacOS/Python scramble.py pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> --------------------------------------------------------------------------- This script requires setuptools version 0.6c11 to run (even to display help). I will attempt to download it for you (from http://pypi.python.org/packages/2.6/s/setuptools/), but you may need to enable firewall access for this script first. I will start the download in 15 seconds. (Note: if this machine does not have network access, please obtain the file http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg and place it in this directory before rerunning this script.) --------------------------------------------------------------------------- Downloading http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ez_setup.py' writing manifest file 'pysam.egg-info/SOURCES.txt' running bdist_egg installing library code to build/bdist.macosx-10.5-i386/egg running install_lib running build_py creating build creating build/lib.macosx-10.5-i386-2.6 creating build/lib.macosx-10.5-i386-2.6/pysam copying pysam/__init__.py -> build/lib.macosx-10.5-i386-2.6/pysam copying pysam/Pileup.py -> build/lib.macosx-10.5-i386-2.6/pysam copying pysam/namedtuple.py -> build/lib.macosx-10.5-i386-2.6/pysam copying pysam/version.py -> build/lib.macosx-10.5-i386-2.6/pysam running build_ext building 'csamtools' extension creating build/temp.macosx-10.5-i386-2.6 creating build/temp.macosx-10.5-i386-2.6/pysam creating build/temp.macosx-10.5-i386-2.6/samtools creating build/temp.macosx-10.5-i386-2.6/samtools/bcftools gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/csamtools.c -o build/temp.macosx-10.5-i386-2.6/pysam/csamtools.o pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_9fetch’: pysam/csamtools.c:8334: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_10mate’: pysam/csamtools.c:8725: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_11count’: pysam/csamtools.c:9212: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_12pileup’: pysam/csamtools.c:9649: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_16IteratorSNPCalls_2__next__’: pysam/csamtools.c:26629: warning: this decimal constant is unsigned only in ISO C90 pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_9SNPCaller_1call’: pysam/csamtools.c:27152: warning: this decimal constant is unsigned only in ISO C90 pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_15IndelCallerBase_2_call’: pysam/csamtools.c:28600: warning: assignment discards qualifiers from pointer target type pysam/csamtools.c: In function ‘__Pyx_InitGlobals’: pysam/csamtools.c:36010: warning: this decimal constant is unsigned only in ISO C90 gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/pysam_util.c -o build/temp.macosx-10.5-i386-2.6/pysam/pysam_util.o pysam/pysam_util.c: In function ‘pysam_pileup_next’: pysam/pysam_util.c:190: warning: assignment discards qualifiers from pointer target type gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam2bcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf_indel.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_aux.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_aux.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_color.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_color.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_import.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_import.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_index.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_lpileup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_lpileup.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_maqcns.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_maqcns.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_mate.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_mate.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_md.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_md.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_pileup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_pileup.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_plcmd.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_plcmd.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_rmdup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdup.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdupse.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_sort.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_sort.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_stat.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_stat.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_tview.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_tview.c.pysam.o samtools/bam_tview.c.pysam.c:420:2: warning: #warning "No curses library is available; tview is disabled." gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bgzf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bgzf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/errmod.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/errmod.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/faidx.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/faidx.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/glf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/glf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kaln.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kaln.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/knetfile.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/knetfile.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kprobaln.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kprobaln.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kstring.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kstring.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/razf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/razf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam_header.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam_header.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam_view.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam_view.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sample.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sample.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf2qcall.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcfutils.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/call1.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/call1.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/fet.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/fet.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/index.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/kfunc.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/ld.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/ld.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/prob1.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/vcf.c.pysam.o gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.1/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/pysam/csamtools.o build/temp.macosx-10.5-i386-2.6/pysam/pysam_util.o build/temp.macosx-10.5-i386-2.6/samtools/bam.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf_indel.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_aux.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_color.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_import.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_index.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_lpileup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_maqcns.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_mate.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_md.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_pileup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_plcmd.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdupse.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_sort.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_stat.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_tview.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bgzf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/errmod.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/faidx.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/glf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kaln.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/knetfile.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kprobaln.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kstring.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/razf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam_header.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam_view.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sample.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcfutils.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/call1.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/fet.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/index.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/kfunc.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/ld.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/prob1.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/vcf.c.pysam.o -lz -o build/lib.macosx-10.5-i386-2.6/csamtools.so building 'ctabix' extension creating build/temp.macosx-10.5-i386-2.6/tabix gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/ctabix.c -o build/temp.macosx-10.5-i386-2.6/pysam/ctabix.o pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__’: pysam/ctabix.c:2666: warning: assignment from incompatible pointer type pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_13TabixIterator_2__next__’: pysam/ctabix.c:2980: warning: assignment discards qualifiers from pointer target type pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__next__’: pysam/ctabix.c:7835: warning: assignment discards qualifiers from pointer target type gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/tabix_util.c -o build/temp.macosx-10.5-i386-2.6/pysam/tabix_util.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/bgzf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/bgzf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/bgzip.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/bgzip.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/index.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/knetfile.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/knetfile.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/kstring.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/kstring.c.pysam.o gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.1/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/pysam/ctabix.o build/temp.macosx-10.5-i386-2.6/pysam/tabix_util.o build/temp.macosx-10.5-i386-2.6/tabix/bgzf.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/bgzip.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/index.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/knetfile.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/kstring.c.pysam.o -lz -o build/lib.macosx-10.5-i386-2.6/ctabix.so creating build/bdist.macosx-10.5-i386 creating build/bdist.macosx-10.5-i386/egg copying build/lib.macosx-10.5-i386-2.6/csamtools.so -> build/bdist.macosx-10.5-i386/egg copying build/lib.macosx-10.5-i386-2.6/ctabix.so -> build/bdist.macosx-10.5-i386/egg creating build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/__init__.py -> build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/namedtuple.py -> build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/Pileup.py -> build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/version.py -> build/bdist.macosx-10.5-i386/egg/pysam byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/namedtuple.py to namedtuple.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/Pileup.py to Pileup.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/version.py to version.pyc creating stub loader for csamtools.so creating stub loader for ctabix.so byte-compiling build/bdist.macosx-10.5-i386/egg/csamtools.py to csamtools.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/ctabix.py to ctabix.pyc creating build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/PKG-INFO -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/SOURCES.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/dependency_links.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/not-zip-safe -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/top_level.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO writing build/bdist.macosx-10.5-i386/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.5-i386.egg' and adding 'build/bdist.macosx-10.5-i386/egg' to it removing 'build/bdist.macosx-10.5-i386/egg' (and everything under it) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pysam did not appear to fail, but no egg found to copy from expected path: /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam/dist/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.5-i386-ucs2.egg paul-tangers-macbook-pro:galaxy-dist paultanger$ On Mon, Aug 29, 2011 at 12:37 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2
Okay, it looks like EPD python is only compiled for one platform. To use this, you'll need to scramble your own versions of the eggs which use C code. Could you try scrambling pysam as instructed below and see what the results are? You will have to do this for each egg that can't be downloaded.
--nate
On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor <nate@bx.psu.edu> wrote:
That worked, for everything but pysam. I also tried to install it
Paul Tanger wrote: directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> 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.
What platform do you get from:
python ./scripts/get_platforms.py
? Note that this needs to have the path changed from append to insert as in the previous scripts.
Thanks, --nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu>
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6? error returned is:
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched 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-0.1-py2.6.egg Fetched
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 32, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
347, in resolve egg.resolve() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
197, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg line line line
228, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu>
wrote:
> Paul Tanger wrote: > > sys path is: > > > > ['/Users/paultanger/galaxy-dist/scripts', > > '/Users/paultanger/python/scripts', > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
> > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > '/Users/paultanger/galaxy-dist/lib'] > > Hi Paul, > > If you replace: > > lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", > "lib" ) ) > sys.path.append( lib ) > > With: > > lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", > "lib" ) ) > sys.path.insert( 0, lib ) > > In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an > effect? > > --nate > > > > > pkg_resources is: > > <module 'pkg_resources' from > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > > > > > > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger < paul.tanger@colostate.edu > >wrote: > > > > > It is free for academic use. I'll try what you suggested below
> thanks! > > > > > > > > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor < nate@bx.psu.edu> wrote: > > > > > >> Paul Tanger wrote: > > >> > Yes it works with the default python install. Any way I can get it > > >> working > > >> > with EPD python? > > >> > > >> I've never worked with EPD and since it's not free it's unlikely we > can > > >> do much debugging on it here. It would appear that they bundle a > > >> version of pkg_resources which changes the DistributionNotFound class, > > >> but it's hard to know exactly what's going on here. > > >> > > >> One thing that might shed a bit of light on it would be to print > > >> sys.path and pkg_resources at the top of: > > >> > > >> galaxy-dist/lib/galaxy/eggs/__init__.py > > >> > > >> After the import of pkg_resources and see which version it's using. > > >> > > >> --nate > > >> > > >> > > > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor < nate@bx.psu.edu> > wrote: > > >> > > > >> > > Paul Tanger wrote: > > >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD > > >> (enthought) > > >> > > python > > >> > > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is > > >> related to > > >> > > the > > >> > > > fact that I have EPD python, not the generic python
wrote: that
was
> > >> > > preinstalled? > > >> > > > Any ideas? > > >> > > > > > >> > > > Thanks! > > >> > > > > > >> > > > Some eggs are out of date, attempting to fetch... > > >> > > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > > >> line > > >> > > > 345, in resolve > > >> > > > egg.resolve() > > >> > > > File > "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > > >> line > > >> > > > 184, in resolve > > >> > > > if e.args[0].project_name != self.distribution.project_name: > > >> > > > AttributeError: 'str' object has no attribute 'project_name' > > >> > > > Fetch failed. > > >> > > > > >> > > Hi Paul, > > >> > > > > >> > > Can you give it a try with the system Python and see if you get > the > > >> same > > >> > > result? All you need to do is put: > > >> > > > > >> > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin > > >> > > > > >> > > At the head of your $PATH. > > >> > > > > >> > > Thanks, > > >> > > --nate > > >> > > > > >> > > >
> > >> > > > 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/ > > >> > > > > >> > > > > >> > > > > > > > > > >
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177 paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
Paul Tanger wrote:
Yes I tried that but it didn't work. The entire output I pasted below in case you are interested. Thanks for your assistance so far, but I think I'm going to give up and just use ubuntu via virtualbox to run galaxy.
Hi Paul, It looks like the egg build succeeded but was probably named differently than expected. The name of the egg built could be determined with: % ls /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam/dist/ Copying this to Galaxy's eggs/ directory probably would not solve the problem since Galaxy will be looking for an egg there with a different name. This could likely be fixed but I don't want to tie up too much of your time. I can also open an issue in the tracker to get it working with EPD Python by setting it up here myself and testing (I didn't notice that it was free for academic use) I won't have a chance to work on this for a while, though. I would think having Galaxy use the system Python would be a quicker/easier solution than a Linux VM, but either approach should work. Sorry you've run in to this trouble. This is the first time I've heard of anyone trying to use it with EPD Python. --nate
paul-tangers-macbook-pro:galaxy-dist paultanger$ python scripts/scramble.py -e pysam
pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
pkg_resources is: <module 'pkg_resources' from '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'> fetch_one(): Using existing source, remove to download again:
/Users/paultanger/galaxy-dist/scripts/scramble/archives/pysam-0.4.2_kanwei_b10f6e722e9a.tar.gz unpack_source(): Removing old build directory at:
/Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam unpack_source(): Unpacked to:
/Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam copy_build_script(): Using build script /Users/paultanger/galaxy-dist/scripts/scramble/scripts/generic.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam:
/Library/Frameworks/Python.framework/Versions/6.1/Resources/Python.app/Contents/MacOS/Python scramble.py
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'>
--------------------------------------------------------------------------- This script requires setuptools version 0.6c11 to run (even to display help). I will attempt to download it for you (from http://pypi.python.org/packages/2.6/s/setuptools/), but you may need to enable firewall access for this script first. I will start the download in 15 seconds.
(Note: if this machine does not have network access, please obtain the file
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg
and place it in this directory before rerunning this script.) --------------------------------------------------------------------------- Downloading http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ez_setup.py' writing manifest file 'pysam.egg-info/SOURCES.txt' running bdist_egg installing library code to build/bdist.macosx-10.5-i386/egg running install_lib running build_py creating build creating build/lib.macosx-10.5-i386-2.6 creating build/lib.macosx-10.5-i386-2.6/pysam copying pysam/__init__.py -> build/lib.macosx-10.5-i386-2.6/pysam copying pysam/Pileup.py -> build/lib.macosx-10.5-i386-2.6/pysam copying pysam/namedtuple.py -> build/lib.macosx-10.5-i386-2.6/pysam copying pysam/version.py -> build/lib.macosx-10.5-i386-2.6/pysam running build_ext building 'csamtools' extension creating build/temp.macosx-10.5-i386-2.6 creating build/temp.macosx-10.5-i386-2.6/pysam creating build/temp.macosx-10.5-i386-2.6/samtools creating build/temp.macosx-10.5-i386-2.6/samtools/bcftools gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/csamtools.c -o build/temp.macosx-10.5-i386-2.6/pysam/csamtools.o pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_9fetch’: pysam/csamtools.c:8334: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_10mate’: pysam/csamtools.c:8725: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_11count’: pysam/csamtools.c:9212: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_7Samfile_12pileup’: pysam/csamtools.c:9649: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_16IteratorSNPCalls_2__next__’: pysam/csamtools.c:26629: warning: this decimal constant is unsigned only in ISO C90 pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_9SNPCaller_1call’: pysam/csamtools.c:27152: warning: this decimal constant is unsigned only in ISO C90 pysam/csamtools.c: In function ‘__pyx_pf_5pysam_9csamtools_15IndelCallerBase_2_call’: pysam/csamtools.c:28600: warning: assignment discards qualifiers from pointer target type pysam/csamtools.c: In function ‘__Pyx_InitGlobals’: pysam/csamtools.c:36010: warning: this decimal constant is unsigned only in ISO C90 gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/pysam_util.c -o build/temp.macosx-10.5-i386-2.6/pysam/pysam_util.o pysam/pysam_util.c: In function ‘pysam_pileup_next’: pysam/pysam_util.c:190: warning: assignment discards qualifiers from pointer target type gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam2bcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf_indel.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_aux.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_aux.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_color.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_color.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_import.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_import.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_index.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_lpileup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_lpileup.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_maqcns.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_maqcns.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_mate.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_mate.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_md.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_md.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_pileup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_pileup.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_plcmd.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_plcmd.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_rmdup.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdup.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdupse.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_sort.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_sort.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_stat.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_stat.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bam_tview.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bam_tview.c.pysam.o samtools/bam_tview.c.pysam.c:420:2: warning: #warning "No curses library is available; tview is disabled." gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bgzf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bgzf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/errmod.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/errmod.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/faidx.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/faidx.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/glf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/glf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kaln.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kaln.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/knetfile.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/knetfile.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kprobaln.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kprobaln.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/kstring.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/kstring.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/razf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/razf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam_header.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam_header.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sam_view.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sam_view.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/sample.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/sample.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf2qcall.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcfutils.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/call1.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/call1.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/fet.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/fet.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/index.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/kfunc.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/ld.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/ld.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/prob1.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/vcf.c.pysam.o gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.1/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/pysam/csamtools.o build/temp.macosx-10.5-i386-2.6/pysam/pysam_util.o build/temp.macosx-10.5-i386-2.6/samtools/bam.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam2bcf_indel.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_aux.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_color.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_import.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_index.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_lpileup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_maqcns.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_mate.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_md.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_pileup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_plcmd.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdup.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_rmdupse.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_sort.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_stat.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bam_tview.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bgzf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/errmod.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/faidx.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/glf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kaln.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/knetfile.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kprobaln.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/kstring.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/razf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam_header.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sam_view.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/sample.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/bcfutils.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/call1.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/fet.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/index.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/kfunc.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/ld.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/prob1.c.pysam.o build/temp.macosx-10.5-i386-2.6/samtools/bcftools/vcf.c.pysam.o -lz -o build/lib.macosx-10.5-i386-2.6/csamtools.so building 'ctabix' extension creating build/temp.macosx-10.5-i386-2.6/tabix gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/ctabix.c -o build/temp.macosx-10.5-i386-2.6/pysam/ctabix.o pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__’: pysam/ctabix.c:2666: warning: assignment from incompatible pointer type pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_13TabixIterator_2__next__’: pysam/ctabix.c:2980: warning: assignment discards qualifiers from pointer target type pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__next__’: pysam/ctabix.c:7835: warning: assignment discards qualifiers from pointer target type gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c pysam/tabix_util.c -o build/temp.macosx-10.5-i386-2.6/pysam/tabix_util.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/bgzf.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/bgzf.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/bgzip.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/bgzip.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/index.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/index.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/knetfile.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/knetfile.c.pysam.o gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.1/include -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/6.1/include/python2.6 -c tabix/kstring.c.pysam.c -o build/temp.macosx-10.5-i386-2.6/tabix/kstring.c.pysam.o gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.1/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/pysam/ctabix.o build/temp.macosx-10.5-i386-2.6/pysam/tabix_util.o build/temp.macosx-10.5-i386-2.6/tabix/bgzf.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/bgzip.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/index.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/knetfile.c.pysam.o build/temp.macosx-10.5-i386-2.6/tabix/kstring.c.pysam.o -lz -o build/lib.macosx-10.5-i386-2.6/ctabix.so creating build/bdist.macosx-10.5-i386 creating build/bdist.macosx-10.5-i386/egg copying build/lib.macosx-10.5-i386-2.6/csamtools.so -> build/bdist.macosx-10.5-i386/egg copying build/lib.macosx-10.5-i386-2.6/ctabix.so -> build/bdist.macosx-10.5-i386/egg creating build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/__init__.py -> build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/namedtuple.py -> build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/Pileup.py -> build/bdist.macosx-10.5-i386/egg/pysam copying build/lib.macosx-10.5-i386-2.6/pysam/version.py -> build/bdist.macosx-10.5-i386/egg/pysam byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/namedtuple.py to namedtuple.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/Pileup.py to Pileup.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/pysam/version.py to version.pyc creating stub loader for csamtools.so creating stub loader for ctabix.so byte-compiling build/bdist.macosx-10.5-i386/egg/csamtools.py to csamtools.pyc byte-compiling build/bdist.macosx-10.5-i386/egg/ctabix.py to ctabix.pyc creating build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/PKG-INFO -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/SOURCES.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/dependency_links.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/not-zip-safe -> build/bdist.macosx-10.5-i386/egg/EGG-INFO copying pysam.egg-info/top_level.txt -> build/bdist.macosx-10.5-i386/egg/EGG-INFO writing build/bdist.macosx-10.5-i386/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.5-i386.egg' and adding 'build/bdist.macosx-10.5-i386/egg' to it removing 'build/bdist.macosx-10.5-i386/egg' (and everything under it) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pysam did not appear to fail, but no egg found to copy from expected path:
/Users/paultanger/galaxy-dist/scripts/scramble/build/py2.6-macosx-10.5-i386-ucs2/pysam/dist/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.5-i386-ucs2.egg paul-tangers-macbook-pro:galaxy-dist paultanger$
On Mon, Aug 29, 2011 at 12:37 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Paul Tanger wrote:
I don't know if I did this correctly, but the output from python get_platforms.py is: macosx-10.5-i386-ucs2
Okay, it looks like EPD python is only compiled for one platform. To use this, you'll need to scramble your own versions of the eggs which use C code. Could you try scrambling pysam as instructed below and see what the results are? You will have to do this for each egg that can't be downloaded.
--nate
On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor <nate@bx.psu.edu> wrote:
That worked, for everything but pysam. I also tried to install it
Paul Tanger wrote: directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: <module 'pkg_resources' from '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> 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.
What platform do you get from:
python ./scripts/get_platforms.py
? Note that this needs to have the path changed from append to insert as in the previous scripts.
Thanks, --nate
On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor <nate@bx.psu.edu>
Paul Tanger wrote: > Getting somewhere, but it looks like it can't find numpy 1.6? > error returned is: > > pkg_resources is: <module 'pkg_resources' from > '/Users/paultanger/galaxy-dist/lib/pkg_resources.py'> > Some eggs are out of date, attempting to fetch... > > pkg_resources is: <module 'pkg_resources' from > '/Users/paultanger/galaxy-dist/lib/pkg_resources.pyc'> > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched > 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-0.1-py2.6.egg > Fetched
> 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 32, in <module> > c.resolve() # Only fetch eggs required by the config > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> 347, in resolve > egg.resolve() > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
> 197, in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py",
http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg line line line
> 228, in version_conflict > r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, > egg.fetch ) > File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in > resolve > raise DistributionNotFound(req) # XXX put more info here > pkg_resources.DistributionNotFound: numpy==1.6.0 > Fetch failed.
It could be a conflict with the existing version, try:
python -ES ./scripts/fetch_eggs.py
--nate
> > On Mon, Aug 29, 2011 at 10:18 AM, Nate Coraor <nate@bx.psu.edu> wrote: > > > Paul Tanger wrote: > > > sys path is: > > > > > > ['/Users/paultanger/galaxy-dist/scripts', > > > '/Users/paultanger/python/scripts', > > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip', > > > '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6', > > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-darwin',
> > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac',
> > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/plat-mac/lib-scriptpackages',
> > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-tk',
> > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-old',
> > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/lib-dynload',
> > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages',
> > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/PIL',
> > > '/Users/paultanger/galaxy-dist/lib'] > > > > Hi Paul, > > > > If you replace: > > > > lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", > > "lib" ) ) > > sys.path.append( lib ) > > > > With: > > > > lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", > > "lib" ) ) > > sys.path.insert( 0, lib ) > > > > In scripts/check_eggs.py and scripts/fetch_eggs.py, does this have an > > effect? > > > > --nate > > > > > > > > pkg_resources is: > > > <module 'pkg_resources' from > > > > >
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
> > > > > > > > > > > > On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger < paul.tanger@colostate.edu > > >wrote: > > > > > > > It is free for academic use. I'll try what you suggested below
> > thanks! > > > > > > > > > > > > On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor < nate@bx.psu.edu> wrote: > > > > > > > >> Paul Tanger wrote: > > > >> > Yes it works with the default python install. Any way I can get it > > > >> working > > > >> > with EPD python? > > > >> > > > >> I've never worked with EPD and since it's not free it's unlikely we > > can > > > >> do much debugging on it here. It would appear that they bundle a > > > >> version of pkg_resources which changes the DistributionNotFound class, > > > >> but it's hard to know exactly what's going on here. > > > >> > > > >> One thing that might shed a bit of light on it would be to print > > > >> sys.path and pkg_resources at the top of: > > > >> > > > >> galaxy-dist/lib/galaxy/eggs/__init__.py > > > >> > > > >> After the import of pkg_resources and see which version it's using. > > > >> > > > >> --nate > > > >> > > > >> > > > > >> > On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor < nate@bx.psu.edu> > > wrote: > > > >> > > > > >> > > Paul Tanger wrote: > > > >> > > > Has anyone gotten galaxy installed on a mac 10.5 with EPD > > > >> (enthought) > > > >> > > python > > > >> > > > 2.6 (EPD version 6.1-1)? I get this error which I suspect is > > > >> related to > > > >> > > the > > > >> > > > fact that I have EPD python, not the generic python
wrote: that
was
> > > >> > > preinstalled? > > > >> > > > Any ideas? > > > >> > > > > > > >> > > > Thanks! > > > >> > > > > > > >> > > > Some eggs are out of date, attempting to fetch... > > > >> > > > 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/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > > > >> line > > > >> > > > 345, in resolve > > > >> > > > egg.resolve() > > > >> > > > File > > "/Users/paultanger/galaxy-dist/lib/galaxy/eggs/__init__.py", > > > >> line > > > >> > > > 184, in resolve > > > >> > > > if e.args[0].project_name != self.distribution.project_name: > > > >> > > > AttributeError: 'str' object has no attribute 'project_name' > > > >> > > > Fetch failed. > > > >> > > > > > >> > > Hi Paul, > > > >> > > > > > >> > > Can you give it a try with the system Python and see if you get > > the > > > >> same > > > >> > > result? All you need to do is put: > > > >> > > > > > >> > > /System/Library/Frameworks/Python.framework/Versions/2.6/bin > > > >> > > > > > >> > > At the head of your $PATH. > > > >> > > > > > >> > > Thanks, > > > >> > > --nate > > > >> > > > > > >> > > >
> > > >> > > > 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/ > > > >> > > > > > >> > > > > > >> > > > > > > > > > > > > > > > > > > -- > _____________________________________ > Paul Tanger > NSF IGERT Bioenergy Fellow > > Bioagricultural Sciences and Pest Management > Colorado State University > 1177 Campus Delivery > Fort Collins, CO 80523-1177 > > paul.tanger@colostate.edu > http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
-- _____________________________________ Paul Tanger NSF IGERT Bioenergy Fellow
Bioagricultural Sciences and Pest Management Colorado State University 1177 Campus Delivery Fort Collins, CO 80523-1177
paul.tanger@colostate.edu http://bioenergy-igert.colostate.edu/
participants (2)
-
Nate Coraor -
Paul Tanger