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Help installing Bioawk

Hello

I've been trying to install bioawk on my ubuntu system however I've come into a few issues.

in my user/bin directory which I've cloned the directory into

sudo git clone https://github.com/lh3/bioawk.git
cd bioawk/
sudo make
./bioawk

./bioawk returns

usage: ./bioawk [-F fs] [-v var=value] [-c fmt] [-tH] [-f progfile | 'prog'] [file ...]

However trying bioawk just returns command not found

I'm aware i may be missing something , this is my first attempt at installing something without a package manager

ubuntu bioawk installation
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updated by dariober dariober • written by 01de • 01de

I just wanted to point out that in this case you don't need sudo to execute git clone and make. In general, it's better to use the super-user powers only when needed.

this is my first attempt at installing something without a package manager

I think installing things yourself is a good exercise but I would suggest getting familiar with conda and bioconda as they take away a lot of headaches. (I assume that by package manager you mean Ubuntu's apt).

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written by dariober dariober

1 answer

You are not missing anything. This is the classic problem of not having the directory which contains the bioawk executable in your system $PATH (a set of directories that are automatically searched when you try to run a program. You can add the directory containing the bioawk executable to $PATH by doing following (for bash shell)

export PATH=$PATH:/path_to_dir_w_bioawk
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written by GenoMax GenoMax

Thank you ! I don't think I'd have been able to work that out on my own.

It seems to be working as expected now.

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written by 01de • 01de

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