Now a bit further along (running a basic workflow on the cluster) and
encountering this problem (see bottom).
This is how the job_conf.xml is setting up:
<destination id="sge_default" runner="sge">
<env file="/opt/rh/python27/enable" />
<param id="nativeSpecification">-V -l h_vmem=2000M</param>
It's an issue with the environment on the compute nodes, but not quite
sure how to solve it.
Traceback (most recent call last):
line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata;
galaxy/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, in
import galaxy.model.mapping # need to load this before we
unpickle, in order to setup properties assigned by the mappers
galaxy/galaxy/lib/galaxy/model/__init__.py", line 21, in <module>
from sqlalchemy import (and_, func, join, not_, or_, select, true,
ImportError: cannot import name true
On Mon, 2017-05-08 at 14:24 +0100, David Simpson wrote:
> Managed to get working by using <env file="/opt/rh/python27/enable"
> On Mon, 2017-05-08 at 10:52 +0100, David Simpson wrote:
> We're close to having a working Galaxy job_conf.xml to submit galaxy
> jobs to an SGE cluster.
> At the moment a submitted job is failing with:
> python: error while loading shared libraries: libpython2.7.so.1.0:
> cannot open shared object file: No such file or directory
> We'd like to solve this by sourcing the dev tools for all our jobs:
> source /opt/rh/python27 enable
> Please could you advise on how to proceed?
> David Simpson
> Systems Engineer
> MRC Centre for Neuropsychiatric Genetics and Genomics
> Cardiff University School of Medicine
> Hadyn Ellis Building
> Maindy Road
> CF24 4HQ
> phone 44 29206 88426
> mail SimpsonD4 at Cardiff.ac.uk
MRC Centre for Neuropsychiatric Genetics and Genomics
Cardiff University School of Medicine
Hadyn Ellis Building
phone 44 29206 88426
mail SimpsonD4 at Cardiff.ac.uk
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