recipe biopet-basecounter

BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.

Homepage:https://github.com/biopet/basecounter
License:MIT
Recipe:/biopet-basecounter/meta.yaml

BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.

For documentation and manuals visit our github.io page: https://biopet.github.io/basecounter

package biopet-basecounter

(downloads) docker_biopet-basecounter

Versions:

0.1-0

Depends:
Required By:

Installation

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

conda install biopet-basecounter

and update with:

conda update biopet-basecounter

or use the docker container:

docker pull quay.io/biocontainers/biopet-basecounter:<tag>

(see biopet-basecounter/tags for valid values for <tag>)

Notes

biopet-basecounter is a Java program that comes with a custom wrapper shell script. By default ‘no default java option’ is set in the wrapper. The command that runs the program is ‘biopet-basecounter’. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with ‘biopet-basecounter -Xms512m -Xmx1g’.