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BUSCO/en: Difference between revisions
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== Available versions == | == 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 [https://gitlab.com/ezlab/busco newer versions], you can install them in your own account using a [[Python#Creating_and_using_a_virtual_environment|virtual environment]] as follows: | |||
{{Commands| | {{Commands| | ||
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and add "home/$USER/busco_env/scripts" to your path. | and add "home/$USER/busco_env/scripts" to your path. | ||
== | == Using BUSCO from CVMFS == | ||
'''1.''' Load the necessary modules: | '''1.''' Load the necessary modules: | ||
{{Command|module load gcc/ | {{Command|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 <code>augustus, blast+, hmmer</code> and some other | |||
software packages that BUSCO relies upon. | |||
'''2.''' Copy the configuration file: | '''2.''' Copy the configuration file: | ||
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[tblastn] | [tblastn] | ||
# path to tblastn | # path to tblastn | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/blast+/2.7.1/bin/ | ||
[makeblastdb] | [makeblastdb] | ||
# path to makeblastdb | # path to makeblastdb | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/blast+/2.7.1/bin/ | ||
[augustus] | [augustus] | ||
# path to augustus | # path to augustus | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/bin/ | ||
[etraining] | [etraining] | ||
# path to augustus etraining | # path to augustus etraining | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | 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 | # path to augustus perl scripts, redeclare it for each new script | ||
[gff2gbSmallDNA.pl] | [gff2gbSmallDNA.pl] | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/ | ||
[new_species.pl] | [new_species.pl] | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/ | ||
[optimize_augustus.pl] | [optimize_augustus.pl] | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/augustus/3.3/scripts/ | ||
[hmmsearch] | [hmmsearch] | ||
# path to HMMsearch executable | # path to HMMsearch executable | ||
path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/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 = /cvmfs/soft.computecanada.ca/easybuild/software/2017/ | path = /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx512/Compiler/gcc7.3/r/4.0.2/bin/ | ||
}} | }} | ||
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{{Command|cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config}} | {{Command|cp -r $EBROOTAUGUSTUS/config $HOME/augustus_config}} | ||
'''5.''' Check that it runs | '''5.''' Check that it runs. | ||
{{Commands | {{Commands | ||
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|run_BUSCO.py --in $EBROOTBUSCO/sample_data/target.fa --out TEST --lineage_path $EBROOTBUSCO/sample_data/example --mode genome | |run_BUSCO.py --in $EBROOTBUSCO/sample_data/target.fa --out TEST --lineage_path $EBROOTBUSCO/sample_data/example --mode genome | ||
}} | }} | ||
The <code>run_BUSCO.py</code> command should take less than 60 seconds to complete. | |||
Production runs which take longer should be submitted to the [[Running jobs|scheduler]]. | |||
= Troubleshooting = | = 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. | ||