Samtools on arm / aws

Hello all,

I haven't been able to find any specific information on this subject so I'm trying my luck here.

I would like to know if it is possible (and how) to use samtools on an ARM architecture? I would indeed like to use it on aws using the graviton processors.

Thanks in advance,

Quentin

samtools arm aws

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updated 4.5 years ago by aw7 •

• written 4.5 years ago by quentin54520 •

Looks like a debian package is available for samtools that supports arm64. You will have to try and see if that works.

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written 4.5 years ago by GenoMax

2 answers

Can't you get it via conda ? https://docs.anaconda.com/anaconda/install/linux-aarch64/

Or does bioconda not support this architecture ?

Edit: No, bioconda does not yet support ARM it seems. https://github.com/bioconda/bioconda-recipes/issues/23454

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written 4.5 years ago by colindaven

We have tested samtools on ARM architecture and it does work.

I have not used AWS Graviton myself so I cannot tell you how to make samtools work there. It does support Ubuntu and Ubuntu does support ARM samtools packages. The Ubuntu LTS releases use outdated versions of samtools (1.10 it looks like). If you want something more modern you are going to have to install it yourself somehow.

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written 4.5 years ago by aw7 •

1.10 not too outdated. Current is 1.14. Those numbers after the period increment sequentially so have been some cause of confusion.

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written 4.5 years ago by GenoMax

You're right. 1.10 came out at the end of 2019 so it hasn't been that long. It just feels longer.

Still, new release out soon.

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written 4.5 years ago by aw7 •