Damona library

Overview

This is the entry point to some damona singularity files. We currently have only a few containers to demonstrate the usage and to serve the purpose of the Sequana project. Damona is a singularity environment manager, not a repository for singularity containers, which can be found in various communties such as the biocontainers.pro registry.

For more information about Damona please see documentation and the github repository.

The goal of damona is to manage singularity files like conda manages pre-compiled packages. Here, to install fastqc v0.11.9 you would simply type:

damona install fastqc:0.11.9

If available on this page, it will be downloaded and stored on your local computer. Binaries will then be available in your PATH. You can manage several environments

damona create --name mytest

and activate it as follows

damona activate mytest

Examples

Here are just two examples of singularity images available in this registry. The full registry is available as a text file to be used by damona.

conda_4.7.12.img (size 306Mb)
fastqc_0.11.8.img (size 198Mb)
fastqc_0.11.9.img (size 198Mb)
rnaseqc_1.3.0.img (size 356Mb)
salmon_1.3.0.img (size 336Mb)
sequana_tools_0.9.0.img (size 1422Mb)

fastqc

Here is the singularity file: fastqc:0.11.9

This tool aims to provide a qc report which can spot problems or biases which originate either in the sequencer or in the starting library material. it can be run in one of two modes. it can either run as a stand alone interactive application for the immediate analysis of small numbers of fastq files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. See also biocontainer

salmon

Here is the singularity file: salmon:1.3.0

Wicked-fast transcript quantification from rna-seq data. See also biocontainer