recipe alphatims

A Python package for indexing Bruker timsTOF raw data

Homepage:

https://github.com/MannLabs/alphatims

Documentation:

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

License:

APACHE / Apache-2.0

Recipe:

/alphatims/meta.yaml

AlphaTims provides fast indexing and slicing of Bruker timsTOF raw data for mass spectrometry-based proteomics.

package alphatims

(downloads) docker_alphatims

versions:

1.0.9-0

depends click:

depends h5py:

depends numba:

depends pandas:

depends psutil:

depends python:

>=3.8

depends pyzstd:

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 alphatims

and update with::

   mamba update alphatims

To create a new environment, run:

mamba create --name myenvname alphatims

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/alphatims:<tag>

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

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Link to this page

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