This repository contains a Dockerfile with specific versions of RNA-seq tools built on top of a specific version of miniconda, for reproducibility purposes. The docker image is built by dockerhub (hub.docker.com/r/pvdb90/rnaseq_tools/) and this will in turn be used to create a Singularity image that works on the Dutch super computer Cartesius using a Singularity file.
| source | tool | version |
|---|---|---|
| continuumio/miniconda | miniconda | 4.5.4 |
| Conda package of fastqc | fastqc | 0.11.7 |
| Conda package of RSEM | rsem | 1.3.1 |
| Conda package of STAR | STAR | 2.6 |
| Conda package of multiqc | multiqc | 1.6 |
| Conda package of kallisto | kallisto | 0.44 |
| Conda package of samtools | samtools | 1.31 |
| Conda package of gffread | gffread | 0.9.9 |
| Conda package of cutadapt | cutadapt | 1.18 |
| Conda package of sickle-trim | sickle-trim | 1.33 |
| Conda package of trimmomatic | Trimmomatic | 0.38 |
1: RSEM (1.3.1) requires samtools version 1.3, even though there is a newer version.