- recipe gapseq
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
- Homepage:
- License:
GPL / AGPL-3.0-only
- Recipe:
gapseq predicts bacterial metabolic pathways and reconstructs genome-scale metabolic models.
After installation, initialize the required databases with:
gapseq update-sequences -t Bacteria gapseq update-sequences -t Archaea
- package gapseq¶
- Versions:
2.1.0-0,2.0.1-0,1.4.0-1,1.4.0-0,1.3.1-0,1.3-0,1.2-0- Depends:
on bc
on bioconductor-biostrings
on blast
on coreutils
on diamond
>=2.1.9on gawk
on glpk
on grep
on hmmer
on libsbml
on openssl
on pyrodigal
on r-base
on r-biocmanager
on r-cobrar
>=0.2.5on r-data.table
on r-getopt
on r-httr
on r-jsonlite
on r-r.utils
on r-rcurl
on r-renv
on r-stringi
on r-stringr
on sed
on wget
- 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 gapseq
to add into an existing workspace instead, run:
pixi add gapseq
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 gapseq
Alternatively, to install into a new environment, run:
conda create -n envname gapseq
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/gapseq:<tag>
(see gapseq/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 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/gapseq/README.html)
