Dear Stéphane,
I can run Python scripts import RDKit modules on CentOS 7 by putting the
following rdkit.conf file in /etc/ld.so.conf.d:
$ cat /etc/ld.so.conf.d/rdkit.conf
/var/www/cgi-bin/rdkit/rdkit-Release_2016_03_1/lib
and adding two SetEnv directives in the <Directory> section of my Apache
rdkit.conf:
$ cat /etc/httpd/conf.d/rdkit.conf
Alias /rdkit /var/www/cgi-bin/rdkit
<Directory /var/www/cgi-bin/rdkit>
SetEnv RDBASE /var/www/cgi-bin/rdkit/rdkit-Release_2016_03_1
SetEnv PYTHONPATH /var/www/cgi-bin/rdkit/rdkit-Release_2016_03_1
[...]
</Directory>
Hope this helps,
Paolo
On 06/21/16 18:05, Téletchéa Stéphane wrote:
> Dear all,
>
> I am willing to incorporate some rdkit functionalities using a django
> backend for an internal project
> (basically ligand annotation and comparison with docking studies) which
> will be published once ready.
>
> Using the "developper" mode of django and conda I can properly get all
> of them working properly,
> but I'm struggling in translating this into a real web service.
>
> For what it counts, I am admin on the machine and for now not a lot of
> services are up so I can test things...
>
> So far I have tried:
> - installing rdkit with conda + all required dependencies + wsgi file
> pointing to it
> - installing django + dependencies using pip + install from scratch of
> rkdit (Ubuntu Linux 14.04 LTS, 64bits):
> a) using a custom location, works with django manage.py runserver
> but not when launched from apache
> b) building rdkit using different locations (adding
> /etc/ld.so.conf.d/rdkit.conf + ldconfig -> libraries are correctly detected)
> c) adding various path in the wsgi.py configuration file
> d) and many more ...
>
> There are other django services working fine on the machine so it does
> not come from there.
> I have also tried to run only this service with no better luck.
>
> I think it is the combination of externally adding LD_LIBRARY_PATH +
> PYTHONPATH that is the culprit,
> since the web server responds to the requested address, but after "a
> certain amout of time", I see in apache2 logs:
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> End of script output before headers: wsgi.py
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Unfortunately there is no other error message, so I am unable to trace
> the rest of the error.
>
> Does it rings a bell to someone?
>
> Thanks a lot in advance,
>
> Stéphane Téletchéa
>
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