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CEMiTool and Docker

The official Docker image for CEMiTool is publicly available on Docker Hub.

This example shows how to use the csblusp/cemitool Docker image with a complete R environment for running CEMiTool. For more information about the CEMiTool analysis workflow, please check the vignette. If you don't have Docker installed, you can follow the steps for your platform here

Initial consideration

All examples shown here will consider a hypothetical /home/me/myanalysis directory which contains your gene expression and sample annotation data.

$ ls /home/me/myanalysis
expression.tsv  sample_annotation.tsv

To make things more practical, we will store this directory in a shell variable called ANALYSIS_DIR

$ export ANALYSIS_DIR=/home/me/myanalysis

Running CEMiTool in interactive mode

With the following command you will be able to access the container in an interactive shell.

$ docker run --rm -it --entrypoint=/bin/bash -v "$ANALYSIS_DIR:$ANALYSIS_DIR" -w $ANALYSIS_DIR -u $(id -u) csblusp/cemitool
docker@1asd8asf1rf3:/home/me/myanalysis/$

Just to make sure you are in the right directory inside the container, take a look at the files in your current directory.

docker@1asd8asf1rf3:/home/me/myanalysis/$ ls
expression.tsv  sample_annotation.tsv

Everything is just fine! Now you can start a R session, load the CEMiTool package and start your analysis.

docker@1asd8asf1rf3:/home/me/myanalysis/$ R -q # Inside the container
> library(CEMiTool) # Load CEMiTool and perform your analysis
> expression_data <- read.table('expression.tsv', sep='\t')
> sample_annotation_data <- read.table('sample_annotation.tsv', sep='\t')

Running CEMiTool from command line

CEMiTool can also be run from the command line, with no need to enter the container. The following command will show the documentation for the command line version of CEMiTool

$ docker run --rm -v "$ANALYSIS_DIR:$ANALYSIS_DIR" -w "$ANALYSIS_DIR" -u $(id -u) csblusp/cemitool --help

The simplest way to run the CEMiTool cli is providing the expression file and --output parameters.

$ docker run --rm -v "$ANALYSIS_DIR:$ANALYSIS_DIR" -w "$ANALYSIS_DIR" -u $(id -u) csblusp/cemitool expression.tsv --output=output_directory

Yeah, I know, this command is lengthy. If you are running on Linux or MacOS, you can set an alias like this:

$ alias cemitool="docker run --rm  -v "$(pwd):$(pwd)" -w "$(pwd)" -u $(id -u) csblusp/cemitool"

Alternativelly, you can download this file and put it into your /usr/local/bin directory.

$ wget https://raw.githubusercontent.com/csbl-usp/CEMiTool/master/docker/cemitool
$ chmod +x cemitool
$ mv cemitool /usr/local/bin

With this you can run CEMiTool container just by calling cemitool on the command line. As you can see, the command is a little different. We changed $ANALYSIS_DIR to $(pwd) just to make the command more general. That being said, in order to run the analysis using this alias you must go to your analysis directory:

$ cd $ANALYSIS_DIR
$ cemitool expression.tsv --output=output_directory

Have fun! 🐳