conda samtools

Question

[PROFESOR]

It gives me error when installing samtools I installed

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
sh Miniconda3-latest-MacOSX-x86_64.sh

conda install -c bioconda samtools 



zsh: command not found: conda
javierpalomares@JAVIERs-Air ~ %

[GenoMax]

I installed

You may have to open a new terminal to have the $PATH amendment (if you chose to do that) come into play. So that is all that may be needed. Open a new terminal and then try conda install. Or try one of the other suggestions.

[4galaxy77]

Possible that installing conda doesn't automatically add the binary to your PATH. Try running ./conda install -c bioconda samtools from where the binary is located or copying the binary to your PATH.

[andres.firrincieli]

you probably need to add the conda directory to the zsh PATH variable.

Try this:

export PATH="~/miniconda3/bin":$PATH

[PROFESOR]

i'm doing that but it keeps happening

javierpalomares@JAVIERs-Air ~ % ls
Desktop                 Movies
Documents               Music
Downloads               Pictures
Library                 Public
Miniconda3-latest-MacOSX-x86_64.sh  miniconda3j


javierpalomares@JAVIERs-Air ~ %  export PATH="~/miniconda3/bin":$PATH
javierpalomares@JAVIERs-Air ~ % conda install -c bioconda samtools
zsh: command not found: javierpalomares@JAVIERs-Air

[andres.firrincieli]

maybe this could help: link

[GenoMax]

It appears that your miniconda3 directory may have a j at the end of it so you will need to modify @andres's command to account for that.

Try

export PATH="~/miniconda3j/bin":$PATH