recipe ssm

Secondary-structure matching, tool for fast protein structure alignment

Homepage:

https://www.ccp4.ac.uk

License:

GPL3 / GPL-3.0-or-later AND LGPL-3.0-or-later

Recipe:

/ssm/meta.yaml

Links:

doi: 10.1107/S0907444904026460

SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI. The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.

package ssm

(downloads) docker_ssm

Versions:

1.4-1,  1.4-0

Depends:

  • on libccp4 >=8.0.0,<9.0a0

  • on libgcc >=13

  • on libstdcxx >=13

  • on mmdb2 >=2.0.22,<3.0a0

  • on pkg-config

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 ssm

to add into an existing workspace instead, run:

pixi add ssm

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 ssm

Alternatively, to install into a new environment, run:

conda create -n envname ssm

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/ssm:<tag>

(see ssm/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 install-with-bioconda 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/ssm/README.html)