It seems that 'namedtuple' is available in python 2.6 (and not older versions :-( as in my case) anyway, thanks for the egg ;-) It works fine Erick 2010/1/27 Erick Antezana <erick.antezana@gmail.com>:
Hi Davide,
thanks for your tips. I was able to get the egg for pysam 0.1.1 (and even for pysam 0.1.2). However, I am facing now another issue, here is the error message:
Traceback (most recent call last): File "./scripts/paster.py", line 33, in ? command.run() File "/galaxy/dev/eggs/py2.4-noplatform/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/galaxy/dev/eggs/py2.4-noplatform/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/galaxy/dev/eggs/py2.4-noplatform/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/galaxy/dev/eggs/py2.4-noplatform/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/galaxy/dev/eggs/py2.4-noplatform/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 188, in invoke filtered = context.next_context.create() File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/galaxy/dev/eggs/py2.4-noplatform/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/galaxy/dev/lib/galaxy/web/buildapp.py", line 69, in app_factory add_controllers( webapp, app ) File "/galaxy/dev/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/galaxy/dev/lib/galaxy/web/controllers/tracks.py", line 26, in ? from galaxy.visualization.tracks.data.bam import BamDataProvider File "/galaxy/dev/lib/galaxy/visualization/tracks/data/bam.py", line 2, in ? from pysam import csamtools File "build/bdist.linux-x86_64/egg/pysam/__init__.py", line 2, in ? File "build/bdist.linux-x86_64/egg/pysam/Pileup.py", line 5, in ? AttributeError: 'module' object has no attribute 'namedtuple'
Any suggestion? (I used Pyrex 0.9.8.5)
thanks in advance, Erick
2010/1/27 Davide Cittaro <davide.cittaro@ifom-ieo-campus.it>:
On Jan 27, 2010, at 11:23 AM, Erick Antezana wrote:
Unfortunately, we have in our system GLIBC 2.5 (glibc-2.5-42.el5_4.2). We have tried to bypass such requirement by compiling pysam and manually copying the csamtools.so file without success. Once I try to launch Galaxy (run.sh) it fetches the original egg (and so library)... The variable FETCH_EGGS was set to 0 but it is still fetching the latest versions...Are we missing something? Otherwise, would it be possible to have such egg for glib 2.5 ?
You may build your pysam version with python setup.py bdist_egg and then copy it to $GALAXYPATH/eggs/py-VERSION-OS-egg/pysam-VERSION-OSRELEASE.egg so next time you run galaxy it will find your egg in the right place with the right name :-) I did it yesterday (for freebsd) d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
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