Damona library

Overview

This is the entry point to some damona singularity files to demonstrate ability to set URL with a registry.txt.

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

This command downloads the container and create binaries on the fly. Binaries will then be available in your PATH. You can manage several environments

damona env --create mytest

and activate it as follows

damona activate mytest

Examples

Here are the singularity images available from this server but more are available in Damona itself.

art_2.5.8.img (size 340Mb)
art_3.11.14.img (size 339Mb)
bcl2fastq_2.20.0.img (size 77Mb)
fastqc_0.11.8.img (size 198Mb)
fastqc_0.11.9.img (size 198Mb)
fitter_1.3.0.img (size 455Mb)
quast_5.0.2.img (size 1399Mb)
rnadiff_1.7.1.img (size 977Mb)
salmon_1.3.0.img (size 336Mb)
sequana_tools_0.10.0.img (size 1677Mb)
sequana_tools_0.11.0.img (size 1682Mb)
sequana_tools_0.12.0.img (size 1371Mb)
sequana_tools_0.9.0.img (size 1422Mb)
trf_4.10.0.img (size 180Mb)
ucsc_0.1.0.img (size 634Mb)

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