Package Recipe 'privateer'

recipe privateer

The Swiss Army knife for carbohydrate structure validation, refinement and analysis

Homepage:: https://github.com/glycojones/privateer
Documentation:: https://www.ccp4.ac.uk/html/privateer.html
License:: LGPL / LGPL-3.0
Recipe:: /privateer/meta.yaml
Links:: doi: 10.1107/S2053230X24000359, doi: 10.1038/nsmb.3115, doi: 10.3762/bjoc.16.204, doi: 10.1107/S2059798323003510

Privateer is a tool for carbohydrate structure validation, re-refinement and graphical analysis. It carries out automatic assignments of ring conformation (IUPAC nomenclature), anomeric form, absolute configuration and comparison to reference values for validation. It computes omit mFo-DFc maps and calculates a correlation coefficient between model and electron density. For structure refinement, it is able to generate chemical dictionaries with unimodal torsion restraints which will help keep the lowest energy conformation. In terms of graphical analysis, it will produce vector diagrams in SNFG nomenclature (SVG format), which are annotated using the validation information (ring conformation, anomeric form, etc). Privateer is implemented in C++11 and Python3 (via pybind11), and produces Scheme and Python scripts for use with Coot (https://github.com/pemsley/coot).

package privateer¶

Versions:

MKV-2, MKV-1, MKV-0

Depends:

on ccp4srs >=2024.6.14
on clipper >=2.1.20180802,<3.0a0
on gemmi <0.6.0
on libccp4 >=8.0.0,<9.0a0
on libgcc >=13
on libgfortran
on libgfortran5 >=13.3.0
on libstdcxx >=13
on matplotlib-base
on mmdb2 >=2.0.22,<3.0a0
on numpy 1.26.*
on prettytable
on pytest
on python >=3.10,<3.11.0a0
on python_abi 3.10.* *_cp310
on requests
on seaborn

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install privateer

to add into an existing workspace instead, run:

pixi add privateer

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install privateer

Alternatively, to install into a new environment, run:

conda create -n envname privateer

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/privateer:<tag>

(see privateer/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/privateer/README.html)