Pysam Egg

Question: Pysam Egg

8.8 years ago by

Erick Antezana • 570 wrote:

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

samtools bam • 1.8k views

ADD COMMENT • link •

modified 8.8 years ago by Davide Cittaro • 140 • written 8.8 years ago by Erick Antezana • 570

8.8 years ago by

Davide Cittaro • 140

Davide Cittaro • 140 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) 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 */

ADD COMMENT • link written 8.8 years ago by Davide Cittaro • 140

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

ADD REPLY • link written 8.8 years ago by Nate Coraor ♦ 3.2k

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

ADD REPLY • link written 8.8 years ago by Nate Coraor ♦ 3.2k

Nate, thanks for the egg. it works fine. Erick 2010/1/27 Nate Coraor <nate@bx.psu.edu>:

ADD REPLY • link written 8.8 years ago by Erick Antezana • 570

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>:

ADD REPLY • link written 8.8 years ago by Erick Antezana • 570

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>:

ADD REPLY • link written 8.8 years ago by Erick Antezana • 570

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.

ADD REPLY • link written 8.8 years ago by James Taylor • 320

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... :-) 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 */

ADD REPLY • link written 8.8 years ago by Davide Cittaro • 140

Similar posts • Search »