Problem solved by using the Galaxy VENV environment instead of RH Dev
tools python27 - changed within the job_conf.xml:

<env file="/opt/rh/python27/enable" />
changed to
<env file="/some/dir/galaxy/.venv/bin/activate" />


As the RH Dev tools python27 has an older sqlalchemy ('0.7.9') vs the
VENV ('1.0.15') ... causing the previous error



On Tue, 2017-05-09 at 11:30 +0100, David Simpson wrote:
> 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 id="SGE_ROOT">/opt/gridengine</env>
> <env file="/opt/rh/python27/enable" />
> <param id="nativeSpecification">-V -l h_vmem=2000M</param>
> </destination>
> 
> 
> It's an issue with the environment on the compute nodes, but not
> quite
> sure how to solve it.
> 
> 
> Traceback (most recent call last):
>   File "/c8000xd2/illumina-cnv-
> galaxy/galaxy/database/jobs_directory/000/711/set_metadata_wAx_ru.py"
> ,
> line 1, in <module>
>     from galaxy_ext.metadata.set_metadata import set_metadata;
> set_metadata()
>   File "/c8000xd2/illumina-cnv-
> galaxy/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, in
> <module>
>     import galaxy.model.mapping  # need to load this before we
> unpickle, in order to setup properties assigned by the mappers
>   File "/c8000xd2/illumina-cnv-
> galaxy/galaxy/lib/galaxy/model/__init__.py", line 21, in <module>
>     from sqlalchemy import (and_, func, join, not_, or_, select,
> true,
> type_coerce,
> 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:
> > Hi,
> > 
> > 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?
> > 
> > regards
> > David
> > 
> > -- 
> > David Simpson
> > Systems Engineer
> > MRC Centre for Neuropsychiatric Genetics and Genomics
> > Cardiff University School of Medicine
> > Hadyn Ellis Building
> > Maindy Road
> > Cardiff
> > CF24 4HQ
> > ------------------
> > phone 44 29206 88426
> > mail SimpsonD4 at Cardiff.ac.uk
-- 
David Simpson
Systems Engineer
MRC Centre for Neuropsychiatric Genetics and Genomics
Cardiff University School of Medicine
Hadyn Ellis Building
Maindy Road
Cardiff
CF24 4HQ
------------------
phone 44 29206 88426
mail SimpsonD4 at Cardiff.ac.uk
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