BUSCO
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BUSCO - Benchmarking sets of Universal Single-Copy Orthologs.
For more information on BUSCO, please see the user manual
Module
Load the needed modules:
[name@server ~]$ module load gcc/5.4.0 busco/3.0.2 blast+/2.6.0 hmmer/3.1b2 augustus/3.2.3/ emboss/6.6.0 r/3.5.0
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
And adapt it (only the last portion is shown):
File : partial_busco_config.ini
[tblastn]
# path to tblastn
path = $EBROOTBLASTPLUS/bin/tblastn
[makeblastdb]
# path to makeblastdb
path = $EBROOTBLASTPLUS/bin/makeblastdb
[augustus]
# path to augustus
path = $EBROOTAUGUSTUS/bin
[etraining]
# path to augustus etraining
path = $EBROOTAUGUSTUS/bin
# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = $EBROOTAUGUSTUS/scripts
[new_species.pl]
path = $EBROOTAUGUSTUS/scripts
[optimize_augustus.pl]
path = $EBROOTAUGUSTUS/scripts
[hmmsearch]
# path to HMMsearch executable
path = $EBROOTHMMER/bin
[Rscript]
# path to Rscript, if you wish to use the plot tool
path = $EBROOTR/bin
Check that it runs:
[name@server ~]$ BUSCO_CONFIG_FILE=$HOME/busco_config.ini run_BUSCO.py -v
BUSCO 3.0.2
or
[name@server ~]$ export BUSCO_CONFIG_FILE=$HOME/busco_config.ini
[name@server ~]$ run_BUSCO.py -v
BUSCO 3.0.2