BUSCO installation and run

Question

[Bioinfonext]

Hi all,

Could anyone please help me how to install Busco using singularity on HPC? Here they have mentioned documentation with docker (https://busco.ezlab.org/busco_userguide.html#docker-image) and also here with singularity (https://wiki.unil.ch/ci/books/service-de-calcul-haute-performance-%28hpc%29/page/running-busco) but still not sure which command to follow for Busco installation.

Many thanks,

[Bioinfonext]

Thanks. it is sorted. Busco installed by using following command;

#download and build image (replacing 5.1.3--pyhdfd78af_0 with latest tag)
singularity pull busco_5.1.3.sif docker://quay.io/biocontainers/busco:5.1.3--pyhdfd78af_0

And now running it with this command, is it correct command with these options? I do have plant fruit transcriptome assembly as input fasta file.

./busco_5.1.3.sif busco -i Trinity.fasta -l eukaryota_odb10 --augustus -o busco_output -m transcriptome

Answer 1

[Philipp Bayer]

That unil.ch link looks a bit too complicated, these are the commands I ran to get BUSCO via Singularity:

Download the image:

singularity pull docker://ezlabgva/busco:v5.2.2_cv1

Run the image with example genome.fasta, assuming it's a genome and a plant:

 singularity run -B $(pwd):/busco_wd/ busco_v5.2.2_cv1.sif busco -l viridiplantae -m genome -i genome.fasta --out results

This will store the temporary files in the current working directory, the -v flag in Docker is the -B flag in Singularity, which means to mount (~connect) your current working directory inside the container as /busco_wd/

You will have a new folder in your working directory called busco_downloads which contains the models from, in this case, the viridiplantae dataset.

[Bioinfonext]

Dear Philipp, thank you so much. I do have de novo assembled transcriptome data. so not sure if it needs any specific options as well.

[Philipp Bayer]

with a transcriptome you'd need to replace the -m genome by -m transcriptome and you should be good to go (see https://busco.ezlab.org/busco_userguide.html#transcriptome-mode-assessing-assembled-transcripts )

Answer 2

[Barry Digby]

On a HPC you will need to use singularity. Docker requires root privileges to run which I'll guess you don't have.

Once you have singularity working try the following command:

singularity pull busco.img docker://ezlabgva/busco:v5.2.2_cv1

I know absolutely nothing about BUSCO so I cannot verify the container, but the Dockerhub page looks very well maintained with new version being released regularly.