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 — Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFB6333WN7L7RQQOEGKWNM3WL7G3TANCNFSM6AAAAAASWC4ZUE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Best, Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley ***@***.*** ***@***.***>