Package Recipe 'coot-headless'

recipe coot-headless

Coot Headless API - Software for macromolecular model building.

Homepage:: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot
Documentation:: https://www.mrc-lmb.cam.ac.uk/lucrezia/libcootapi-documentation/index.html
Developer docs:: https://github.com/pemsley/coot
License:: GPL3 / GPL-3.0-or-later AND LGPL-3.0-or-later
Recipe:: /coot-headless/meta.yaml
Links:: doi: 10.1107/S0907444910007493

Coot is a macromolecular model building, model completion and validation application. This package provides the headless APIs (Chapi python bindings and libcootapi C++ library) without GUI dependencies, suitable for automated workflows.

package coot-headless¶

Versions:

1.1.20-1, 1.1.20-0, 1.1.19-0, 1.1.18-3, 1.1.18-2, 1.1.18-1, 1.1.18-0, 1.1.17-3, 1.1.17-2,

1.1.20-1, 1.1.20-0, 1.1.19-0, 1.1.18-3, 1.1.18-2, 1.1.18-1, 1.1.18-0, 1.1.17-3, 1.1.17-2, 1.1.17-1, 1.1.17-0

Depends:

on cairo >=1.18.4,<2.0a0
on clipper >=2.1.20180802,<3.0a0
on elfutils >=0.191,<0.192.0a0
on fontconfig >=2.15.0,<3.0a0
on fonts-conda-ecosystem
on gemmi >=0.7.4,<0.7.5.0a0
on gsl >=2.7,<2.8.0a0
on libboost >=1.86.0,<1.87.0a0
on libccp4 >=8.0.0,<9.0a0
on libffi >=3.4.6,<3.5.0a0
on libfreetype >=2.14.1
on libfreetype6 >=2.14.1
on libgcc >=13
on libpng >=1.6.54,<1.7.0a0
on libsqlite >=3.51.2,<4.0a0
on libstdcxx >=13
on libxml2 >=2.13.9,<2.14.0a0
on libzlib >=1.3.1,<2.0a0
on mmdb2 >=2.0.22,<3.0a0
on numpy 1.26.*
on numpy >=1.26.4,<2.0a0
on pixman >=0.46.4,<1.0a0
on python >=3.10,<3.11.0a0 *_cpython
on python_abi 3.10.* *_cp310
on rdkit
on servalcat
on ssm >=1.4,<2.0a0

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 coot-headless

to add into an existing workspace instead, run:

pixi add coot-headless

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 coot-headless

Alternatively, to install into a new environment, run:

conda create -n envname coot-headless

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/coot-headless:<tag>

(see coot-headless/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/coot-headless/README.html)