romanhaa/penncnv repository overview

⁠Overview

This image allows you to run PennCNV scripts from whatever system you are using without having to install older Perl and gcc versions. The original PennCNV website can be found here: http://penncnv.openbioinformatics.org/en/latest/⁠

Note: To keep the image size small, it doesn't contain any R (which means visualize_cnv.pl won't be able to export jpegs).

⁠Use

There are two ways to run the scripts:

1. Directly when starting the container

docker run -v /src/dir:/target/dir romanhaa/penncnv detect_cnv.pl [ARGS]

1. From the shell in the container

docker run -it --rm -v /src/dir:/target/dir romanhaa/penncnv bash
detect_cnv.pl [ARGS]

Note: To make your input accessible for the scripts in the container it is necessary to mount the respective folder, which is what '-v' is doing. Keep that in mind when defining the path of input and output files.

It also includes the additional reference files and scripts for Affymetrix array analysis.

All relevant PennCNV files are located in: /opt/PennCNV-1.0.5

⁠News

• 2020-02-12
  • PennCNV has been updated to v1.0.5.
  • Image was generated using a Dockerfile (https://github.com/romanhaa/docker_containers/tree/master/PennCNV/1.0.5⁠)

Feedback is more than welcome, especially since I haven't been able to try the image on other machines yet. On mine it works without errors.