Hi, I've just updated my Galaxy install. Everything works fine. I only had an issue while trying to use the pysam egg. The error message is the following: ImportError: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home/bio/erick/.python-eggs/pysam-0.1.1-py2.4-linux-x86_64.egg-tmp/pysam/csamtools.so) 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 ? thanks, Erick
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 */
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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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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I think we're working around this, but you need to make sure you are building from our modified pysam: http://bitbucket.org/kanwei/kanwei-pysam I can't see any good reason why this should have a dependency on glib, but in any case we try to build all eggs with static linking, so we'll fix this. On Jan 27, 2010, at 11:22 AM, Erick Antezana wrote:
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
On Jan 27, 2010, at 5:22 PM, Erick Antezana wrote:
It seems that 'namedtuple' is available in python 2.6 (and not older versions :-( as in my case)
Mmm... why on earth are you using python 2.4? Are you on RedHat / CentOS distribution? I've built the egg on CentOS 5.3, using native python...
anyway, thanks for the egg ;-) It works fine
:-) Glad to hear that! 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 */
Davide Cittaro wrote:
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)
Even simpler, you should be able to 'python scripts/scramble.py pysam' from the root of the galaxy distribution. I have new glibc 2.3 eggs in the pipeline that should be up on the distribution site soon, as well. --nate
Nate Coraor wrote:
I have new glibc 2.3 eggs in the pipeline that should be up on the distribution site soon, as well.
In fact, they're up now. Anyone experiencing this issue should remove the pysam egg from their appropriate subdirectory of eggs/ and then: % python scripts/fetch_eggs.py --nate
Nate, thanks for the egg. it works fine. Erick 2010/1/27 Nate Coraor <nate@bx.psu.edu>:
Nate Coraor wrote:
I have new glibc 2.3 eggs in the pipeline that should be up on the distribution site soon, as well.
In fact, they're up now. Anyone experiencing this issue should remove the pysam egg from their appropriate subdirectory of eggs/ and then:
% python scripts/fetch_eggs.py
--nate _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
participants (4)
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Davide Cittaro -
Erick Antezana -
James Taylor -
Nate Coraor