recipe gnali

gNALI (gene nonessentiality and loss-of-function identifier) is a tool for finding PLoF gene variants.



APACHE / Apache-2.0



package gnali

(downloads) docker_gnali



depends ensembl-vep:

depends filelock:

depends git:


depends htslib:

depends numpy:

depends pandas:

depends perl-bio-bigfile:

depends progress:

depends py-bgzip:

depends pybiomart:

depends pysam:


depends python:


depends python-magic:

depends pyyaml:

depends samtools:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install gnali

and update with::

   mamba update gnali

To create a new environment, run:

mamba create --name myenvname gnali

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `gnali/tags`_ for valid values for ``<tag>``)

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