Can salmon be made available for ARM based arch

[tamuanand]

Hi @rob-p

A question: Can salmon be made available for ARM based arch?

Context: AWS has recently launched instances with ARM based processors which claim to have better performance.

I would like to test/use salmon workflows with ARM based instances.

Thanks in advance,

[tamuanand]

Hi @rob-p

Thanks for the thanksgiving release of salmon. We saw salmon 1.3.0 for July 4th, salmon 1.4.0 for Thanksgiving, hopefully we would see 1.5.0 for Christmas and 1.6.0 for New Year :)

Keep up the great work.

I see that you have salmon now available for ARM machines - https://github.com/COMBINE-lab/salmon/releases/tag/v1.4.0

As myself and @patrick-douglas has requested here - https://github.com/COMBINE-lab/salmon/issues/424 - the ability to compile salmon on ARM is great

A question: Will this work if I do a bioconda install or do I need to compile using the tar.gz file. I am using the ARM based conda from https://github.com/Archiconda/build-tools/releases/download/0.2.3/Archiconda3-0.2.3-Linux-aarch64.sh and with that I could do

conda config --add channels c4aarch64 && conda config --add channels defaults && conda config --add channels anaconda && conda config --add channels bioconda && conda config --add channels conda-forge 
 
conda install -c bioconda -c conda-forge -y nextflow bbmap numpy fastqc

I don't see arch64 for salmon in bioconda here - https://anaconda.org/bioconda/salmon

[rob-p]

Hi @tamuanand,

Yes, we had just about finished up a nice set of features and I thought it would be fun to have another holiday-themed release :). I'm not sure if we'll hit all of the holidays but we definitely have more stuff in the pipeline over the next few months.

Currently, the ARM build has to be compiled from source. I asked a leader of the bioconda team about automatically compiling ARM binaries through the mainstream bioconda and having them be part of the package management system. They told me this isn't currently possible, but that capability should exist early next year. Once it's feasible upstream in the main bioconda, we'll have ARM executables built as well. For the time being, building from source is probably the easiest way. We may also make a pre-compiled ARM binary (e.g. on an AWS machine), though that will have limited compatibility, so its not as preferred as building from source.

[tamuanand]

Hi @rob-p

Wishing you a very Happy New Year. I wanted to check if you would have a pre-compiled ARM binary on an AWS machine as suggested here:

We may also make a pre-compiled ARM binary (e.g. on an AWS machine), though that will have limited compatibility

Thanks