How to install Pyteomics¶
Supported Python versions¶
Pyteomics supports Python 2.7 and Python 3.3+.
Install with pip¶
The main way to obtain Pyteomics is via pip Python package manager:
pip install pyteomics
Install with conda¶
You can also install Pyteomics from Bioconda using conda:
conda install -c bioconda pyteomics
Arch-based distros¶
On Arch Linux and related distros, you can install Pyteomics from AUR: python-pyteomics
Project dependencies¶
Some functionality in Pyteomics relies on other packages:
- numpy;
- matplotlib (used by
pyteomics.pylab_aux);- lxml (used by XML parsing modules and
pyteomics.mass.mass.Unimod);- pandas (can be used with
pyteomics.pepxml,pyteomics.tandem,pyteomics.mzid,pyteomics.auxiliary);- sqlalchemy (used by
pyteomics.mass.unimod);- pynumpress (adds support for Numpress compression in mzML);
- h5py and optionally hdf5plugin (used by
pyteomics.mzmlb);- psims (used py
pyteomics.proforma);- spectrum_utils (optionally used for spectrum annotation in
pyteomics.pylab_aux).
All dependencies are optional.
Installing a subset of dependencies with pip¶
You can quickly install just the dependencies you need by specifying an “extra”. For example:
pip install pyteomics[XML]
This will install Pyteomics, NumPy and lxml, which are needed to read XML format. Currently provided identifiers are: XML, TDA, graphics, DF, Unimod, numpress, mzMLb, proforma.
You can also use these specs as dependencies in your own packages which require specific Pyteomics functionality.