- recipe gapseq
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
- Homepage:
- License:
GPL / AGPL-3.0-only
- Recipe:
- package gapseq¶
- Versions:
1.4.0-1,1.4.0-0,1.3.1-0,1.3-0,1.2-0- Depends:
on barrnap
on bc
on bedtools
on bioconductor-biostrings
on blast
on coreutils
on exonerate
on gawk
on git
on glpk
on grep
on hmmer
on libsbml
on openssl
on parallel
on perl
on r-base
on r-biocmanager
on r-cobrar
on 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¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/gapseq/README.html)
