Provide native binaries for all programs on all platforms

[victorlin]

Progress tracker

• MAFFT
• IQ-TREE: Run IQ-TREE natively in ARM64 image #212
• Nextalign/Nextclade v1
• tsv-utils
• gofasta
• minimap2

Background

Currently, each of these programs are downloaded using one binary for all both available platforms amd64 and arm64. Since there is more widespread support for emulation of amd64 binaries on an arm64 host, the amd64 binaries are downloaded.

This means that for arm64 hosts, amd64 emulation must be used to run these programs. The most common use case is running the Nextstrain Docker runtime on an Apple silicon Mac computer. These computers support the necessary emulation using Rosetta 2, however note that emulation can result in slower run times compared to running with the native binary.

Potential solutions

In preferred order:

1. Download dynamically based on TARGET* variables
   1. Official binaries
   2. Unofficial binaries
2. Build from source.

[victorlin]

This might still be good to do at some point, but things are working fine with the current setup. Closing for now.

[corneliusroemer]

conda-forge/bioconda have native linux-aarch64 for all of these:

• mafft
• iqtree
• tsv-utils
• gofasta