Use this directory for testing the pipeline on a protein sample.

Type here:

./setup.sh


To see the status of the setup:

./orthologer.sh -xp

It will produce a lengthy output and if all is well, it should not produce any error
and terminate with a 'all checks passed'.

If anything fails, it is most likely related to the external tool paths:

DIR_BRHCLUS
DIR_CDHIT
DIR_MMSEQS
DIR_BLAST

Update them in the common.sh file.

Once the checks pass, the pipeline can be run using:

./run_full_test.sh

This will run through the pipeline until the end or an error.
Typically the run should take in the order of one minute. But timing will
vary strongly with the nr of cores available.
It will also compare the result with a reference.

It can be stopped at any time by pressing 'ctrl-c'.
