recipe spectra-cluster-cli

This is a stand-alone implementation of the new updated PRIDE Cluster algorithm. It is based on the spectra-cluster API and uses a highly similar logic as the Hadoop implementation spectra-cluster-hadoop used to build the PRIDE Cluster resource.

Homepage

https://github.com/spectra-cluster/spectra-cluster-cli

License

Apache / Apache-2.0

Recipe

/spectra-cluster-cli/meta.yaml

package spectra-cluster-cli

(downloads) docker_spectra-cluster-cli

Versions

1.1.2-0, 1.0.1-1, 1.0.1-0

Depends openjdk

>=6

Depends python

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install spectra-cluster-cli

and update with:

conda update spectra-cluster-cli

or use the docker container:

docker pull quay.io/biocontainers/spectra-cluster-cli:<tag>

(see spectra-cluster-cli/tags for valid values for <tag>)

Notes

spectra-cluster-cli is Java program that comes with a custom wrapper shell script. This shell wrapper is called “opsin” and is on $PATH by default. By default “-Xms512m -Xmx1g” 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 “spectra-cluster-cli -Xms512m -Xmx1g”