software container

Introduction

This image contains some of the most popular software used at Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.

Software is versioned by making use of Environment Modules.

Additionally to the standard bioinformatics tools, there is also a Jupyter and RStudio server installation.

The Jupyter installation comes with Python 2, Python 3, and R kernels ready to go.

The container is available from the docker hub.

Usage

Create a folder to map to the container's user home folder

mkdir -p ~/bioinf-container

Start the container from the latest version of the image

sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/bioinf-container:/home/mpiage --name bioinf-container \
-it mpgagebioinformatics/bioinformatics_software:latest

Alternatively you can start the container from a specific tag/version of the image

sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/bioinf-container:/home/mpiage --name bioinf-container \
-it mpgagebioinformatics/bioinformatics_software:<tag>

Connect to the running container

sudo docker exec -i -t bioinf-container /bin/bash

Stop the container

sudo docker stop bioinf-container

Jupyter

Once you have connected to the running container you can start jupyter with

module load jupyterhub
jupyter notebook --ip=0.0.0.0

A URL will be presented to you, and it should be pasted into your host's browser (Chrome recommended).

For using the ruby kernel you will have to get your kernel registered by running once

module load jupyterhub
iruby notebook

RStudio-server Once you have connected to the running container you can start Rstudio server with

module load rlang
sudo rstudio-server start

You can then get access by connecting on your host's browser to http://localhost:8787.

For stopping the server use:

sudo rstudio-server stop

X forward

On a Mac install socat and xquartz:

brew install socat
brew install xquartz

Open Xquartz:

open -a Xquartz

Then navigate to XQuartz > Preferences > Security and tick the box 'Allow connections from network clients'.

Check your ip address:

IP=$(ifconfig en0 | grep inet | awk '{ print $2 }')

Start socat:

socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\"

an then start the container by adding the -e DISPLAY=${IP}:0 argument.

Complete example call:

IP=$(ifconfig en0 | grep inet | awk '{ print $2 }') && \
socat TCP-LISTEN:6000,reuseaddr,fork UNIX-CLIENT:\"$DISPLAY\" & \
docker run -d -e DISPLAY=${IP}:0 -p 8787:8787 -p 8888:8888 \
-v ~/bioinf-container:/home/mpiage --name bioinf-container \
-it mpgagebioinformatics/bioinformatics_software:latest

User account

User: mpiage

Pass: bioinf

Note : As only the home folder in the guest container gets mapped to the local host, all files NOT placed IN the home folder will be lost if the container is removed.

Environment Modules Project

A centralized software system. The modules system loads software (version of choice) and changes environment variables (eg. LD_LIBRARY_PATH).

show available modules: module avail
show a description of the samtools module: module whatis samtools
show environment changes for samtools: module show samtools
load default samtools version: module load samtools
load specific samtools version: module load samtools/1.2.1
list all loaded modules: module list
unload the samtools module: module unload samtools
unload all loaded modules: module purge

Versioning/Tags

All images are released with the following tag structure:

<major release>.<changed system package>.<changed software module>

v3.0.0:

container:~$ module avail
------------------------------- /modules/modulefiles/bioinformatics -------------------------------
bamutil/1.0.14(default)        hisat/2.1.0(default)      samtools/0.1.19            
bcl2fastq/2.20.0.422(default)  homer/4.11.0(default)     samtools/1.9.0(default)    
bedtools/2.29.0(default)       igor/1.3.0(default)       segemehl/0.2.0(default)    
blast/2.9.0(default)           igrec/3.1.1(default)      seqtk/1.3.0(default)       
bowtie/1.2.3                   iseerna/1.2.2(default)    skewer/0.2.2(default)      
bowtie/2.3.5(default)          kallisto/0.46.1(default)  snpeff/4.3.t(default)      
bwa/0.7.17(default)            kenttools/390(default)    spades/3.11.1(default)     
bwtool/face601(default)        lofreq/2.1.3(default)     sratoolkit/2.9.6(default)  
cufflinks/2.2.1(default)       meme/5.1.0(default)       star/2.7.3a(default)       
cytoscape/3.7.2(default)       methpipe/3.4.3(default)   stringtie/2.0.4(default)   
emboss/6.6.0(default)          mitools/1.5.0(default)    subread/2.0.0(default)     
epiteome/1.0.0(default)        ngsutils/0.5.9(default)   tophat/2.1.1(default)      
expat/2.2.9(default)           picard/2.21.4(default)    trimmomatic/0.39(default)  
fastqc/0.11.8(default)         primer3/2.5.0(default)    vcftools/0.1.16(default)   
flexbar/3.5.0(default)         quast/5.0.2(default)      vdjtools/1.2.1(default)    
gatk/4.1.4(default)            rsem/1.3.1(default)       walt/1.1.0(default)        

---------------------------------- /modules/modulefiles/general -----------------------------------
jdk/13.0.1(default)   jupyterhub/1.0.0(default)  python/2.7.16(default)  rlang/3.6.1(default)  
jre/8.0.231(default)  perl/5.28.1(default)       python/3.8.0            

------------------------------------ /modules/modulefiles/libs ------------------------------------
bzip2/1.0.8(default)  imagemagick/7.0.9-7(default)  xz/5.2.4(default)  
gsl/2.6.0(default)    openblas/0.3.7(default)

Shifter/Singularity

Shifer and Singularity users should add the following line to their host ~/.bashrc:

if [[ -e /home/mpiage/.bashrc ]] ; then

module() { eval `/usr/bin/modulecmd bash $*`; }
export -f module

MODULESHOME=/usr/share/Modules
export MODULESHOME

if [ "${LOADEDMODULES:-}" = "" ]; then
    LOADEDMODULES=
      export LOADEDMODULES
fi

if [ "${MODULEPATH:-}" = "" ]; then
    MODULEPATH=`sed -n 's/[       #].*$//; /./H; $ { x; s/^\n//; s/\n/:/g; p; }' ${MODULESHOME}/init/.modulespath`
      export MODULEPATH
fi

if [ ${BASH_VERSINFO:-0} -ge 3 ] && [ -r ${MODULESHOME}/init/bash_completion ]; then
   . ${MODULESHOME}/init/bash_completion
fi

fi

if [[ -e /home/mpiage/.bashrc ]]; then module purge; unset PYTHONHOME PYTHONUSERBASE PYTHONPATH; source /home/mpiage/.bashrc; fi

Contributing

Clone this repo:

git clone https://github.com/mpg-age-bioinformatics/software_docker.git

Make a new version folder in agreement with Versioning/Tags:

cd software_docker
mkdir v1.0.1
cd v1.0.1
touch Dockerfile

Generate the content of the Dockerfile making sure that on the "FROM" you are using the key for latest available version and using the examples from previous Dockerfiles.

Build the image:

docker build -t mpgagebioinformatics/bioinformatics_software:<version_tag>

Try the image and test respective changes

mkdir -p ~/bioinf-container

sudo docker run -d -p 8787:8787 -p 8888:8888 \
-v ~/bioinf-container:/home/mpiage --name bioinf-container \
-it mpgagebioinformatics/bioinformatics_software:<version_tag>

sudo docker exec -i -t bioinf-container /bin/bash

Push your changes to the repo on github (it will push a docker image with the latest tag).

Add the new version tag (e.g. v1.2.3) to push you docker image with the version tag:

git tag -e -a <version tag> HEAD
git push
git push origin --tags

Python and perl Modules should be installed by the user with the --user option. If modules are needed for the installation of software on module environment they should be installed inside the package. Example:

  echo "setenv PYTHONUSERBASE $SOFT/package/1.0.0/lib/python2.7" >> $MODF/bioinformatics/quast/4.6.0 && \
  echo "prepend-path PERL5LIB $SOFT/package/1.0.0/lib/perl5" >> $MODF/bioinformatics/quast/4.6.0