BUSCO/en: Difference between revisions
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BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs". | BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs". | ||
It is an application for assessing genome assembly and annotation completeness. | It is an application for assessing genome assembly and annotation completeness. | ||
For more information see the [https://gitlab.com/ezlab/busco/blob/master/BUSCO_v3_userguide.pdf user manual] | For more information see the [https://gitlab.com/ezlab/busco/blob/master/BUSCO_v3_userguide.pdf user manual]. | ||
== Usage == | == Usage == | ||
Load the | '''1.''' Load the necessary modules: | ||
{{Command|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}} | {{Command|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: | '''2.''' Copy the configuration file: | ||
{{Command|cp -v $EBROOTBUSCO/config/config.ini.default $HOME/busco_config.ini}} | {{Command|cp -v $EBROOTBUSCO/config/config.ini.default $HOME/busco_config.ini}} | ||
or | or | ||
{{Command|wget -O $HOME/busco_config.ini https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default}} | {{Command|wget -O $HOME/busco_config.ini https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default}} | ||
Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below: | '''3.''' Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below: | ||
{{File | {{File | ||
|name=partial_busco_config.ini | |name=partial_busco_config.ini | ||
| Line 54: | Line 54: | ||
}} | }} | ||
Copy the Augustus config directory to a writable location: | '''4.''' Copy the Augustus config directory to a writable location: | ||
{{Command|cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config}} | {{Command|cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config}} | ||
Check that | '''5.''' Check that it runs: | ||
{{Commands | {{Commands | ||
| Line 65: | Line 65: | ||
}} | }} | ||
= | = Troubleshooting = | ||
== Cannot write to Augustus config path == | == Cannot write to Augustus config path == | ||
Make sure you have copied the config directory to a writable location and exported the <tt>AUGUSTUS_CONFIG_PATH</tt> variable. | Make sure you have copied the config directory to a writable location and exported the <tt>AUGUSTUS_CONFIG_PATH</tt> variable. | ||
Revision as of 22:25, 16 January 2019
BUSCO stands for "Benchmarking sets of Universal Single-Copy Orthologs".
It is an application for assessing genome assembly and annotation completeness.
For more information see the user manual.
Usage
1. Load the necessary modules:
[name@server ~]$ 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
2. Copy the configuration file:
[name@server ~]$ cp -v $EBROOTBUSCO/config/config.ini.default $HOME/busco_config.ini
or
[name@server ~]$ wget -O $HOME/busco_config.ini https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default
3. Edit the configuration file. The locations of external tools are all specified in the last section, which is shown below:
File : partial_busco_config.ini
[tblastn]
# path to tblastn
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin
[makeblastdb]
# path to makeblastdb
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin
[augustus]
# path to augustus
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/bin
[etraining]
# path to augustus etraining
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/bin
# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts
[new_species.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts
[optimize_augustus.pl]
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts
[hmmsearch]
# path to HMMsearch executable
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/hmmer/3.1b2/bin
[Rscript]
# path to Rscript, if you wish to use the plot tool
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/r/3.5.0/bin
4. Copy the Augustus config directory to a writable location:
[name@server ~]$ 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
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.