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.
- 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 serverwith
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=${IP}:0 -p 8787:8787 -p 8888:8888 \
-v ~/bioinf-container:/home/mpiage --name bioinf-container \
-it mpgagebioinformatics/bioinformatics_software:latest
- User account
User: mpiage
Pass: bioinf
Note : As only the home folder in the guest container gets mapped to the local host, all files NOT placed IN the home folder will be lost if the container is removed.
A centralized software system. The modules system loads software (version of choice) and changes environment variables (eg. LD_LIBRARY_PATH).
- show available modules:
module avail - show a description of the samtools module:
module whatis samtools - show environment changes for samtools:
module show samtools - load default samtools version:
module load samtools - load specific samtools version:
module load samtools/1.2.1 - list all loaded modules:
module list - unload the samtools module:
module unload samtools - unload all loaded modules:
module purge
All images are released with the following tag structure:
<major release>.<changed system package>.<changed software module>
- v3.0.0:
container:~$ 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)
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; fiClone this repo:
git clone https://github.com/mpg-age-bioinformatics/software_docker.gitMake a new version folder in agreement with Versioning/Tags:
cd software_docker
mkdir v1.0.1
cd v1.0.1
touch DockerfileGenerate 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/bashPush 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 --tagsPython 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