recipe encyclopedia

EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis

Homepage:

https://bitbucket.org/searleb/encyclopedia/wiki/Home

License:

APACHE / Apache License 2.0

Recipe:

/encyclopedia/meta.yaml

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

(downloads) docker_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 fonts-conda-ecosystem:

depends openjdk:

>=11

depends python:

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 encyclopedia

and update with::

   mamba update encyclopedia

To create a new environment, run:

mamba create --name myenvname encyclopedia

with myenvname being 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/encyclopedia:<tag>

(see `encyclopedia/tags`_ for valid values for ``<tag>``)

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"

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