#
Install Harpy
Harpy is hosted on Bioconda, which means you just need to have either conda
or pixi
(or docker
) on your Unix-like
system to install it.
It's best to create a new environment for a harpy installation. The code below creates a new conda/mamba environment called harpy
(via -n harpy
) and installs harpy into it. You can name this environment whatever you like using the -n somename
argument.
conda create -n harpy -c bioconda -c conda-forge harpy
Once conda/mamba finishes, activate the harpy conda/mamba environment with:
conda activate env_name
where env_name
is the name of that environment. After doing so, the harpy
executable should be callable from your path.
Alternatively, you can create the environment locally within a specific project folder, just swap -n harpy
for
-p path/to/workdir/harpy
, which creates the environment in that specific folder (e.g. potato_blight/harpy
).
conda create -p path/to/workdir/harpy -c bioconda -c conda-forge harpy
If you wish to install harpy and its dependencies into an existing environment, activate that environment and execute this installation code:
conda activate env_name
conda install -c conda-forge bioconda::harpy
Or provide -n env_name
to install it into an existing environment named env_name
conda install -n env_name -c conda-forge bioconda::harpy
Activate the environment and run conda update
:
conda update -c conda-forge bioconda::harpy
#
⚡ Conda Usage
Activate the conda environment with Harpy and call harpy
or harpy --help
on the command line to get started
conda activate harpy_env
# or, if installed locally
conda activate path/to/harpy_env
harpy
If you prefer Pixi (it's pretty good, you should try it), you can install Harpy to be accessible in your PATH, i.e. a "global" installation:
pixi global install -c conda-forge -c bioconda harpy
add pixi to PATH
Make sure ~/.pixi/bin
is in your PATH:
export PATH=~/.pixi/bin:$PATH
Likewise, you can do an installation into a local project directory:
pixi init -c conda-forge -c bioconda projectname && cd projectname
pixi add harpy
If installed via Pixi, you can update Harpy with pixi update
:
# global install
pixi global update harpy
# local install
# project dir has the pixi.toml file
cd path/to/projectdir
pixi update harpy
#
⚡ Pixi Usage
If installed globally, just call harpy
or harpy --help
on the command line, otherwise navigate to the directory with the pixi environment and call harpy from within it:
# installed globally
harpy
# navigate to project directory
cd path/to/workdir
# activate the pixi environment and run harpy
pixi shell
harpy
# or prepend `pixi run` to it without activating the environment
pixi run harpy
If you didn't know, packages on Bioconda are automatically built as containers too! So, if you're using docker, you can pull the Harpy container using:
docker pull quay.io/biocontainers/harpy
Then proceed to use containerized-Harpy however you are used to using containers on your system.