This repo contains the main Dockerfiles which I use regularly in bioinformatics analysis. Images are available at Docker Hub.

Feel free to use these docker images and if you have any questions message me at [email protected].

Here is a brief description of all current software.

This image contains software for RNA sequencing (RNA-Seq) analysis. It's based on tidyverse 3.4.4, which is a complete R solution to tidy data. The added Bioconductor packages are intended to perform gene expression exploration with DESeq2 and also transform and annotate the gene IDs between GENCODE and NCBI. It also contains tximport, a package to import count tables from pseudo-alignment programs. Extra packages are:

• DESeq2
• tximport
• GenomicFeatures
• ensembldb
• org.Hs.eg.db
• pheatmap
• IHW
• vsn
• rjson

Docker Pull Command: docker pull rcoan/tidyverse-deseq2

Run as rocker/tidyverse (mounting your current directory to the container):

docker run -d --rm -p 8787:8787 -v $(PWD):/home/rstudio rcoan/tidyverse-deseq2

(for a different password add -e PASSWORD=yourpassword)

Then type in browser:

localhost:8787

user/password: rstudio/rstudio

PLEK 1.2 for lncRNA discovery.

Docker Pull Command: docker pull rcoan/plek

FEELnc is a program to identify and classify new lncRNA. It is fast and accurate. This image is based on version 0.1.1 - Paper.

Docker Pull Command: docker pull rcoan/feelnc

FEELnc has three modules runned separetly in a terminal window.

docker run -w /mnt -v $(PWD):/mnt --rm rcoan/feelnc FEELnc_filter.pl <OPTIONS> > <OUTPUT_FILE>

docker run -w /mnt -v $(PWD):/mnt --rm rcoan/feelnc FEELnc_codpot.pl <OPTIONS>

docker run -w /mnt -v $(PWD):/mnt --rm rcoan/feelnc FEELnc_classifier.pl <OPTIONS> > <OUTPUT_CLASSES.TXT>

All options found in the manual can be added.

The above commands mount your current directory to the container.

This image contains the WGCNA Bioconductor package for co-expression network construction. It is based on tidyverse 3.6 and no extra packages.

Docker Pull Command: docker pull rcoan/wgcna

Run as rocker/tidyverse (mounting your current directory to the container):

docker run -d -p 8787:8787 -e PASSWORD=wgcna -v $(PWD):/home/rstudio rcoan/wgcna

Then type in browser:

localhost:8787

user/password: rstudio/wgcna

RNA-Seq reads simulator Polyester 1.22. Link to Bioconductor and GitHub. Based on rocker/tidyverse 3.6.

Docker Pull Command: docker pull rcoan/polyester

Run as rocker/tidyverse (mounting your current directory to the container):

docker run -d --rm -p 8787:8787 -e PASSWORD=poly -v $(PWD):/home/rstudio rcoan/polyester

Then type in browser:

localhost:8787

user/password: rstudio/poly