Last Sunday, with the Memoir gang, we were talking about using this blog as a technical notebook. This post is in that spirit.

We have moved most of the validation of Memoir before submitting the job to the queue.  This has the advantage that the user knows immediately the submission has failed (instead of waiting for the job to be processed in the queue).  The only issue with this is that the apache user (on most systems www-data) is going to run the validation pipeline.  Memoir requires a ton of PATH variables addition.

In most cases you cannot add variables in .bashrc as the apache user does not have a home directory.  The easiest way how to add environment variables for the apache user is:

sudo vim /etc/apache2/envvars

And add the following line at the bottom (these have to be customized according to the server):

export PATH=$PATH:/opt/tmalign:/opt/muscle:/opt/joy-5.10:/opt/joy-5.10/psa:/opt/joy_related-1.06:/opt/joy_related-1.06/sstruc:/opt/joy_related-1.06/hbond:/opt/medeller-dev/bin:/opt/usearch6.0.307:/opt/ncbi-blast-2.2.27+:/opt/MPT/bin

After this restart apache – and you should be laughing. Or, as is often the case, apache will be laughing at you.

sudo service apache2 restart

The apache user should now “see” the amended path variable.

Here it is this technical note – so in a few weeks time when I forget all of the above I can just copy and paste it …

(This post is short, also because there is the superbowl!!)