Hi David,
It sounds like you may have installed the version of pbs-python currently in PyPI, which includes a copy of the Torque C library that is not "manylinux"-safe (it is not backwards compatible to older systems). The solution here is to install pbs-python from its source distribution:
1. Activate Galaxy's virtualenv: `. /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/bin/activate` 2. `pip uninstall pbs-python` 3. Download/unpack the source tarball from ftp://ftp.surfsara.nl/pub/outgoing/pbs_python.tar.gz 4. In the pbs_python source: `./configure --prefix=/panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv` 5. `make install`
--nate
On Thu, Nov 17, 2016 at 11:08 AM, David Lee david.lee@bristol.ac.uk wrote:
Hi,
I'm trying to install Galaxy version 16.07 on a cluster with the PBS job scheduler that is using glibc version 2.12. The following error message suggests that pbs-python needs at least glibc version 2.14 -
assert pbs is not None, PBS_IMPORT_MESSAGEAssertionError: The Python pbs-python package is required to use this feature, please install it or correct the following error:
ImportError /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /panfs/panasas01/dedicated-galaxy/galaxy/galaxy/.venv/ lib/python2.7/site-packages/pbs/_pbs.so)
I'm told by an administrator of the cluster that updating to glibc version 2.14 or higher would require a major overhaul of all the software on the cluster. Does anybody have a workaround for this problem? Could a newer version of glibc be used next to version 2.12 just for installation purposes?
Thanks for your help, David
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