- recipe upimapi
UniProt Id Mapping through API
- Homepage:
- Documentation:
- License:
BSD / BSD-3-Clause
- Recipe:
UPIMAPI takes as input either a list of UniProt IDs or a blast file from annotation using UniProt database as reference and uses UniProt's API to retrieve information relative to those IDs. It is essentially a command line implementation of UniProt's ID mapping web service available at https://www.uniprot.org/uploadlists/, allowing for retrieval of information from thousands of IDs in one go, while still relying on the web service.
- package upimapi¶
- Versions:
1.13.3-0,1.13.1-0,1.13.0-0,1.12.3-0,1.12.2-0,1.12.1-0,1.12.0-0,1.11.2-0,1.11.1-0,1.13.3-0,1.13.1-0,1.13.0-0,1.12.3-0,1.12.2-0,1.12.1-0,1.12.0-0,1.11.2-0,1.11.1-0,1.11.0-0,1.10.0-0,1.9.0-0,1.8.14-0,1.8.13-0,1.8.12-0,1.8.11-0,1.8.10-0,1.8.9-0,1.8.8-0,1.8.7-0,1.8.6-0,1.8.5-0,1.8.4-0,1.8.3-0,1.8.2-0,1.8.1-0,1.7.5-0,1.7.4-0,1.7.3-0,1.7.2-0,1.7.1-0,1.7.0-0,1.6.4-0,1.6.3-0,1.6.2-0,1.6.1-0,1.6.0-0,1.5.2-0,1.5.1-0,1.5.0-0,1.4.0-0,1.3.0-0,1.2.2-0,1.2.1-0,1.2.0-0,1.1.4-0,1.1.3-1,1.1.3-0,1.1.2-0,1.1.1-0,1.1.0-0,1.0.4-0,1.0.3-0,1.0.2-0- Depends:
on biopython
on diamond
on pandas
on psutil
on pyyaml
on requests
on tqdm
- 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 upimapi
to add into an existing workspace instead, run:
pixi add upimapi
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 upimapi
Alternatively, to install into a new environment, run:
conda create -n envname upimapi
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/upimapi:<tag>
(see upimapi/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/upimapi/README.html)
