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_MESSAGE

AssertionError: 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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