recipe alphabase

An infrastructure Python package of the AlphaX ecosystem

Homepage:

https://github.com/MannLabs/alphabase

Documentation:

https://alphabase.readthedocs.io/en/latest/

License:

APACHE / Apache-2.0

Recipe:

/alphabase/meta.yaml

AlphaBase provides foundational data structures and utilities for mass spectrometry-based proteomics in the AlphaPept ecosystem.

package alphabase

versions:

1.8.1-0

depends biopython:

depends contextlib2:

depends h5py:

depends lxml:

depends numba:

depends numpy:

depends pandas:

depends pyahocorasick:

depends pyarrow:

depends pyteomics:

depends python:

>=3.9

depends python-xxhash:

depends pyyaml:

depends rdkit:

depends regex:

depends tqdm:

requirements:

additional platforms:

Installation

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 alphabase

and update with::

   mamba update alphabase

To create a new environment, run:

mamba create --name myenvname alphabase

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 quay.io/biocontainers/alphabase:<tag>

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

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