Running Busco

A Singularity container is available for version 4.0.6 of Busco. To run it, you need to proceed as follows:

$ source /dcsrsoft/spack/bin/setup_dcsrsoft
$ module load singularity
$ export SINGULARITY_BINDPATH="/scratch,/users"

Some configuration files included in the container must be copied in a writable location. So create a directory in your /scratch, e.g. called "busco_config"

$ mkdir /path/to/busco_config

Then we copy the stuff out of the container to the newly created directory:

$ singularity exec /dcsrsoft/singularity/containers/busco-4.0.6 cp -rv /opt/miniconda/config/. /path/to/busco_config

Now we need to set the AUGUSTUS_CONFIG_PATH environment variable to the newly created and populated busco_config directory:

$ export AUGUSTUS_CONFIG_PATH=/path/to/busco_config

Finally, you should now be able to run a test dataset from busco (see https://gitlab.com/ezlab/busco/-/tree/master/test_data/eukaryota):

$ curl -O https://gitlab.com/ezlab/busco/-/raw/master/test_data/eukaryota/genome.fna

And launch the analysis. 
Note: in $AUGUSTUS_CONFIG_PATH you have a copy of the default config.ini used here, so you can copy, modify it and use it in the --config option in the following command:

$ singularity exec /dcsrsoft/singularity/containers/busco-4.0.6 busco --config /opt/miniconda/config/config.ini -i genome.fna -c 8 -m geno -f --out test_eukaryota

Then download the reference log:

curl -O https://gitlab.com/ezlab/busco/-/raw/master/test_data/eukaryota/expected_log.txt

And compare to the one you generated.

 

 

 


Revision #8
Created 22 January 2021 07:56:38 by Etienne Orliac
Updated 3 February 2021 11:48:23 by Etienne Orliac