- 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:
1.3.1-0,1.3-0,1.2-0- depends barrnap:
- depends bc:
- depends bedtools:
- depends bioconductor-biostrings:
- depends blast:
- depends coreutils:
- depends exonerate:
- depends gawk:
- depends git:
- depends glpk:
- depends grep:
- depends hmmer:
- depends libsbml:
- depends openssl:
- depends parallel:
- depends perl:
- depends r-base:
- depends r-biocmanager:
- depends r-chnosz:
- depends r-data.table:
- depends r-doparallel:
- depends r-foreach:
- depends r-getopt:
- depends r-glpkapi:
- depends r-httr:
- depends r-jsonlite:
- depends r-r.utils:
- depends r-rcurl:
- depends r-renv:
- depends r-stringi:
- depends r-stringr:
- depends r-sybil:
- depends sed:
- depends wget:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install gapseq and update with:: mamba update gapseq
To create a new environment, run:
mamba create --name myenvname gapseq
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/gapseq:<tag> (see `gapseq/tags`_ for valid values for ``<tag>``)
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Link to this page¶
Render an 
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