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BUSCO/en: Difference between revisions
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To see the latest available version, run: | To see the latest available version, run: | ||
{{Command|avail_wheel busco}} | {{Command|avail_wheel busco}} | ||
== Python | == Python wheels == | ||
=== Installation === | === Installation === | ||
<b>1.</b> Load the necessary modules: | |||
{{Commands | {{Commands | ||
|module load StdEnv/2020 gcc python/3.10 augustus hmmer blast+ metaeuk prodigal r}} | |module load StdEnv/2020 gcc python/3.10 augustus hmmer blast+ metaeuk prodigal r}} | ||
<b>2.</b> Create the virtual environment: | |||
{{Commands | {{Commands | ||
|virtualenv busco_env | |virtualenv busco_env | ||
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}} | }} | ||
<b>3.</b> Install the wheel and its dependencies: | |||
{{Command | {{Command | ||
|prompt=(busco_env) $ | |prompt=(busco_env) $ | ||
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==== Test ==== | ==== Test ==== | ||
<b>4.</b> Download test data: | |||
{{Commands | {{Commands | ||
|wget https://gitlab.com/ezlab/busco/-/raw/master/test_data/bacteria/genome.fna | |wget https://gitlab.com/ezlab/busco/-/raw/master/test_data/bacteria/genome.fna | ||
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}} | }} | ||
<b>5.</b> Run: | |||
{{Command|busco --offline --in genome.fna --out TEST --lineage_dataset bacteria_odb10 --mode genome --cpu ${SLURM_CPUS_PER_TASK-1} }} | {{Command|busco --offline --in genome.fna --out TEST --lineage_dataset bacteria_odb10 --mode genome --cpu ${SLURM_CPUS_PER_TASK-1} }} | ||
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=== Slurm tips === | === Slurm tips === | ||
Specify < | Specify <code>--offline</code> to avoid using internet. | ||
Specify < | Specify <code>--cpu</code> to <code>$SLURM_CPUS_PER_TASK</code> in your job submission script to use the number of CPUs allocated. | ||
Specify < | Specify <code>--restart</code> to restart from a partial run. | ||
== Modules == | == Modules == | ||
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= 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 < | Make sure you have copied the config directory to a writable location and exported the <code>AUGUSTUS_CONFIG_PATH</code> variable. | ||