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Why I can't use "hmmbuild" command

I have downloaded hmmer 3.3.2 version. My system is Win10 and I try to use Gitbash to run command "hmmbuild" but it doesn't work. It shows that "hmmbuild: command not found". I have added the path for hmmbuild:

"F:\hmmer-3.3.2\src\hmmbuild.c"

into the system environment path. I really wonder what's wrong with this process.

hmmer
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updated by Mensur Dlakic Mensur Dlakic • written by brgs • brgs

I have added the path for hmmbuild:

you didn't. This is the path to the source code of a C program that must be compiled.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks for reply. I think you are right but there is no other hmmbuild file in that directory. Do you mean that I need to run something to configure that?

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written by brgs • brgs

1 answer

You are pointing at a "C" source of the program (thus that .c at the end), which is a humanized version of instructions that computer programs are running. It needs to be compiled into executable form (sometimes called binary form), which is a program that computer understands and can run. If you have no idea what I am talking about, this may help:

https://open.oregonstate.education/computationalbiology/chapter/installing-bioinformatics-software/

Note that contrary to descriptions in the above webpage, http://hmmer.org/download.html does not distribute executables any more. There used to be even a Windows version, but my guess is that it became too difficult to maintain. HMMer suite of programs (and indeed many other bioinformatics applications) are not written with Windows users in mind, and are not necessarily Windows-friendly.

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written by Mensur Dlakic Mensur Dlakic

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