recipe cfm-id

CFM-ID 4 - Competitive Fragmentation Modeling for MS/MS prediction and metabolite identification

Homepage:

https://cfmid.wishartlab.com/

Developer docs:

https://bitbucket.org/wishartlab/cfm-id-code

License:

LGPL / LGPL-2.1-only

Recipe:

/cfm-id/meta.yaml

Links:

doi: 10.1021/acs.analchem.1c01465, doi: 10.1093/nar/gkac383

CFM-ID applies Competitive Fragmentation Modeling to predict ESI-MS/MS spectra from molecular structures, to annotate peaks, and to rank candidate structures against an experimental spectrum.

This package provides the CFM-ID 4 generation. The older `cfm` package (version 33) is CFM-ID 3-era software; the two install binaries with the same names and cannot be installed together.

Pretrained CFM-ID 4 parameters are installed under $PREFIX/share/cfm-id-<version>/. The upstream repository also ships ~172 MB of cross-validation models, which are not needed at runtime and are deliberately not packaged.

package cfm-id#

(downloads) docker_cfm-id

Versions:

4.4.10-0

Depends:

  • on __glibc >=2.17,<3.0.a0

  • on boost-cpp

  • on libgcc >=14

  • on liblbfgs >=1.10,<1.11.0a0

  • on libstdcxx >=14

  • on lp_solve 5.5.*

  • on rdkit >=2021.03.1,<2024

Additional platforms:

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 cfm-id

to add into an existing workspace instead, run:

pixi add cfm-id

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 cfm-id

Alternatively, to install into a new environment, run:

conda create -n envname cfm-id

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/cfm-id:<tag>

(see cfm-id/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/cfm-id/README.html)