How to run pre-msa.bf

[NicMAlexandre]

Hi I installed hyphy-analyses per the instructions like so:

module load gcc openmpi git clone https://github.com/veg/hyphy.git hyphy-develop cd hyphy-develop git checkout develop cmake -DZLIB_LIBRARY="/global/scratch/users/nalexandre/miniconda3/lib/libz.a" -DZLIB_INCLUDE_DIR="/global/scratch/users/nalexandre/miniconda3/lib/" ./ make -j MP ./HYPHYMP analysis-file --help

I am trying to figure out how to run pre-msa.bf, but I cannot find it in the directory following installation nor can I run the executable when I download it manually.

[spond]

Dear @nicolasalexandre21,

The sequence above installs the HyPhy program and standard libraries. pre-msa is a part of standalone analyses (hyphy-analyses) that need to be installed separately. I just realized that the README there did not include this step. I've updated it now: see https://github.com/veg/hyphy-analyses/blob/master/README.md

Best, Sergei

[NicMAlexandre]

Ah this is perfect! Thank you!

On Tue, Dec 6, 2022 at 3:54 PM Sergei Pond @.***> wrote:

Dear @nicolasalexandre21 https://github.com/nicolasalexandre21,

The sequence above installs the HyPhy program and standard libraries. pre-msa is a part of standalone analyses (hyphy-analyses) that need to be installed separately. I just realized that the README there did not include this step. I've updated it now: see https://github.com/veg/hyphy-analyses/blob/master/README.md

Best, Sergei

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