Linked-read data processing pipeline. Getting you from raw linked reads to assemblies, genotypes, or phased haplotypes. Batteries included 🔋
✨ Now works with TELLseq, stLFR, and non-linked read data! ✨
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.
⬇️ install as local conda environment
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
).
# for local project directory
conda create -p path/to/workdir/harpy -c bioconda -c conda-forge harpy
⬇️ install into existing conda environment
If you wish to install harpy and its dependencies into an existing environment, activate that environment (conda activate env_name
) and execute this installation code:
conda install -c conda-forge bioconda::harpy
Or provide -n envname
to install it into an existing environment named envname
conda install -n envname -c conda-forge bioconda::harpy
⬆️ updating harpy
If installed via conda, you can update Harpy by activating the environment
and running conda update
like so:
conda update -c conda-forge bioconda::harpy
If you prefer Pixi (it's pretty good, you should try it), you can install Harpy to be accessible in your PATH:
🌟 how to install pixi
# install pixi
curl -fsSL https://pixi.sh/install.sh | bash
# add this to ~/.zshrc or ~/.bashrc (or equivalent)
export PATH=~/.pixi/bin:$PATH
pixi global install -c conda-forge -c bioconda harpy
⬇️ install harpy into local environment
Likewise, you can do an installation into a local project directory:
pixi init -c conda-forge -c bioconda projectname && cd projectname
pixi add harpy
After that finishes, you can activate the environment with:
pixi shell
Or run harpy
by prefixing it with pixi run
:
pixi run harpy
⬆️ updating 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
Just call harpy
or harpy --help
on the command line to get started!
harpy
No data? No problem! Harpy lets you simulate genomic variants from an existing genome and can also create linked-read data from an existing genome! You can see what haplotagging (or other linked read) data and Harpy are like without paying a cent! A simple tutorial on simulating both of these can be found here.