- recipe encyclopedia
EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis
- Homepage:
- License:
APACHE / Apache License 2.0
- Recipe:
- Links:
biotools: encyclopedia, doi: 10.1038/s41467-018-07454-w
EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. Check out our manuscript describing EncyclopeDIA at Nature Communications (Searle et al, 2018) for more information. EncyclopeDIA contains Walnut, an implementation of the PECAN (Ting et al, 2017) scoring system, to enable chromatogram library generation from FASTA protein sequence databases when spectrum libraries are unavailable.
- package encyclopedia¶
- Versions:
2.12.30-0,1.12.34-0,1.2.2-0,0.9.5-3,0.9.5-2,0.9.5-1,0.9.5-0,0.9.0-0- Depends:
on fonts-conda-ecosystem
on openjdk
>=11on python
- 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 encyclopedia
to add into an existing workspace instead, run:
pixi add encyclopedia
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 encyclopedia
Alternatively, to install into a new environment, run:
conda create -n envname encyclopedia
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/encyclopedia:<tag>
(see encyclopedia/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.
Notes¶
EncyclopeDIA is Java program that comes with a custom wrapper python shell script. This shell wrapper is called "EncyclopeDIA" and is on $PATH by default. By default "-Xms1g -Xmx8g" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with "EncyclopeDIA -Xms512m -Xmx16g"
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/encyclopedia/README.html)
