BUSCO
BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs".
It is an application for assessing genome assembly and annotation completeness.
For more information see the user manual.
Available versions
Version 3.0.2 of BUSCO is installed as a module on CVMFS and accessible on all clusters. See below how to use it.
For the newer versions, you can install them in your own account using a virtual environment as follows:
[name@server ~]$ ~ $ module load python/3.7.4
~ $ git clone https://gitlab.com/ezlab/busco.git
~ $ virtualenv /home/$USER/busco_env
~ $ source /home/$USER/busco_env/bin/activate
(busco_env) [~]$ pip install Biopython
(busco_env) [~]$ cd ~/busco
(busco_env) [~]$ python setup.py install
(busco_env) [~]$ cp -r scripts test_data /home/$USER/busco_env/
and add "home/$USER/busco_env/scripts" to your path.
Using BUSCO from CVMFS
1. Load the necessary modules:
[name@server ~]$ module load StdEnv/2018.3 gcc/7.3.0 openmpi/3.1.4 busco/3.0.2 r/4.0.2
This will also load modules for augustus, blast+, hmmer and some other
software packages that BUSCO relies upon.
2. Copy the configuration file:
[name@server ~]$ cp -v $EBROOTBUSCO/config/config.ini.default $HOME/busco_config.ini
or
[name@server ~]$ wget -O $HOME/busco_config.ini https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default
3. Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below:
[tblastn]
# path to tblastn
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/blast+/2.7.1/bin/
[makeblastdb]
# path to makeblastdb
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/blast+/2.7.1/bin/
[augustus]
# path to augustus
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/bin/
[etraining]
# path to augustus etraining
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/bin/
# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/
[new_species.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/
[optimize_augustus.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/
[hmmsearch]
# path to HMMsearch executable
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/hmmer/3.1b2/bin/
[Rscript]
# path to Rscript, if you wish to use the plot tool
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/r/4.0.2/bin/
4. Copy the Augustus config directory to a writable location:
[name@server ~]$ cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config
5. Check that it runs.
[name@server ~]$ export BUSCO_CONFIG_FILE=$HOME/busco_config.ini
[name@server ~]$ export AUGUSTUS_CONFIG_PATH=$HOME/augustus_config
[name@server ~]$ run_BUSCO.py --in $EBROOTBUSCO/sample_data/target.fa --out TEST --lineage_path $EBROOTBUSCO/sample_data/example --mode genome
The run_BUSCO.py command should take less than 60 seconds to complete.
Production runs which take longer should be submitted to the scheduler.
Troubleshooting
Cannot write to Augustus config path
Make sure you have copied the config directory to a writable location and exported the AUGUSTUS_CONFIG_PATH variable.