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BUSCO/en: Difference between revisions
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{{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. | 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 23: | Line 23: | ||
[tblastn] | [tblastn] | ||
# path to tblastn | # path to tblastn | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin | ||
[makeblastdb] | [makeblastdb] | ||
# path to makeblastdb | # path to makeblastdb | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin | ||
[augustus] | [augustus] | ||
# path to augustus | # path to augustus | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/bin | ||
[etraining] | [etraining] | ||
# path to augustus etraining | # path to augustus etraining | ||
path = | 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 | # path to augustus perl scripts, redeclare it for each new script | ||
[gff2gbSmallDNA.pl] | [gff2gbSmallDNA.pl] | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts | ||
[new_species.pl] | [new_species.pl] | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts | ||
[optimize_augustus.pl] | [optimize_augustus.pl] | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/augustus/3.2.3/scripts | ||
[hmmsearch] | [hmmsearch] | ||
# path to HMMsearch executable | # path to HMMsearch executable | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/hmmer/3.1b2/bin | ||
[Rscript] | [Rscript] | ||
# path to Rscript, if you wish to use the plot tool | # path to Rscript, if you wish to use the plot tool | ||
path = | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/r/3.5.0/bin | ||
}} | }} | ||
Copy the Augustus config directory to a writable location: | |||
{{Command| | {{Command|cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config}} | ||
}} | |||
Check that its runs: | |||
{{Commands | {{Commands | ||
|export BUSCO_CONFIG_FILE{{=}}$HOME/busco_config.ini | |export BUSCO_CONFIG_FILE{{=}}$HOME/busco_config.ini | ||
|run_BUSCO.py - | |export AUGUSTUS_CONFIG_PATH{{=}}$HOME/augustus_config | ||
|run_BUSCO.py --in $EBROOTBUSCO/sample_data/target.fa --out TEST --lineage_path $EBROOTBUSCO/sample_data/example --mode genome | |||
}} | }} | ||
= Troubleshoot = | |||
== 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. | |||