For us, it was more the fact that we are locked down to a certain OS
version due to our local IT policy and the software repositories don't
provide a newer Python than v2.6.8. It was not the first occasion in terms
of desperately outdated software (recently it's gcc itself), so we are
used to compile from source. Using pre-compiled packages from OpenSUSE
repos is not guaranteed to work properly. For us, it is just another
(larger) paragraph for our setup environment written in Ansible. Overall,
it is quite generic and nearly everything needed by Galaxy is installed in
home scheme.
On top, although we are in a quite tight internal network, we realized
that our OpenSSL is of 'pre-heartbleed' times, so it was a good deal to
re-integrate that. Python, wget and others take advantage from this update
if properly linked. Certificate exchange and SSL version usage have moved
on in the last years, and from time to time we got errors/warnings when
accessing external servers.


> On Wed, Mar 23, 2016 at 10:54 PM, D K <danielforti...@gmail.com> wrote:
>> Great! thanks for the suggestions. I just tried using centos software
>> collections and that seems to work. I'll do some more testing but
>> hopefully
>> it's as simple as that! Is there any reason that most of you who
>> responded
>> have decided to compile your own pythons?
>>
>> D
>
> It sounds like both options are effective.
>
> In my case it was perhaps a choice out of ignorance about just how the
> CentOS software collections works - and fear about the CentOS 6 to 7
> migration.
>
> In our case both the Galaxy server and the cluster is still on CentOS 6,
> so we need to use a custom Python 2.7 on both the Galaxy server and
> also on the cluster nodes - ideally the exact same version so that all
> the wheel dependencies match up for running the set metadata scripts.
>
> I'm hoping that using a custom Python 2.7 installation (from source)
> ought to work in our favour if we have to deal with a mixture of CentOS
> 6 and 7 (although ideally we'd update the cluster and Galaxy server
> together).
>
> Regards,
>
> Peter
>


-- 
Sebastian Schaaf, M.Sc. Bioinformatics
Faculty Coordinator NGS Infrastructure
Chair of Biometry and Bioinformatics
Department of Medical Informatics,
 Biometry and Epidemiology (IBE)
University of Munich
DKTK Munich
Marchioninistr. 15, K U1 808
D-81377 Munich (Germany)
Tel: +49 89 4400 77499

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