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iqbal-lab-org / make_prg

Code to create a PRG from a Multiple Sequence Alignment file
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MAFFT is portable for linux and we can embed it into make_prg #50

Closed leoisl closed 1 year ago

leoisl commented 1 year ago

See https://mafft.cbrc.jp/alignment/software/linuxportable.html

Like this, make_prg dependencies are all python deps, and there is no need to install mafft anymore

mbhall88 commented 1 year ago

Just wondering how necessary this is? If people use the conda package or container then they don't need to worry about mafft anyway.

Not saying don't do it; just saying it seems low priority to me?

leoisl commented 1 year ago

That's true, should have thought about this before finishing the core code yesterday... Is useful just for the pip and binary users. I think conda is the most used manager by bionformaticians, but if they don't use conda, will likely fall back to pip or the binary. I might be wrong, but I have a feeling that container users are just a small fraction

leoisl commented 1 year ago

mafft is required in PATH to run integration tests, and this was sth that bothered me... so might be worth it to do this...

leoisl commented 1 year ago

Closed via https://github.com/iqbal-lab-org/make_prg/pull/52