mahshaaban/analysis_containers repository overview

⁠Overview

This repository contains images of the modified containers used to run different workflow to reproduce the analyses of several projects. The containers are mainly based on bioconductor/release_base2⁠, and with the additional required R packages installed. Each image is a the latest modified container with the minimum requirements to reproduce a single analysis. Tags are the reference for such analysis and not different versions of the same image.

⁠A general workflow

The repository is intended to be used along with git and overleaf in three consecutive steps:

• pull and run the docker image

$ docker pull mahshaaban/analysis_containers:$analysis_tag
$ docker run -it -v $(pwd):/home/rstudio mahshaaban/analysis_containers:$analysis_tab bash

where; $analysis_tab is the tag from this repository referring to a particular analysis (e.g. bio_wgcna) and $(pwd) is the path to the current working directory or any directory within it.

• clone the GitHub repository containing the analysis scripts

$ git clone $github_repo

where; $github_repo is the url for the GitHub repository containing the analysis scripts of a certain analysis (e.g https://github.com/MahShaaban/autophagy_ampk⁠).

• From within the cloned repo, build the directory tree and run the R scripts

$ cd $github_repo
$ mkdir data figures tables
$ Rscript R/$analysis_scripts
$ Rscript R/$figures
$ Rscript R/$tables

where; $github_repo is the cloned directory (e.g. autophagy_ampk) in the previous example and R/$analysis_scripts, R/$figures and R/$tables are the names of the analysis, figures and tables scripts and usually in the R/ directory (e.g. R/analysis_script.R).

Alternatively, the scripts can be run and modified alternatively using Rsutio Server which is shipped with the images.

$ docker run -it -p 8787:8787 -v $(pwd):/home/rstudio mahshaaban/analysis_containers:$analysis_tab

And Rstudio Server will be available at port localhost:8787 in the web browser.

⁠Contents

This is intended to be an updated list of the contents of the repository. Each entry contains a tag, update date, description, and contents in that order.

• bioc_wgcna updated 2018/01/19 A portable environment based on bioconductor/release_base2 to reproduce the analysis in the article (). Contains the following packages: GO.db, org.Mm.eg.db, RSQLite, GEOmetadb, GEOquery, purrr, WGCNA, GEOquery, tidyverse, reshape2, rafalib, igraph, limma, clusterProfiler, STRINGdb, xlsx, xtable, cowplot

⁠Contacts

email: [email protected]⁠