Skip to content

This docker app is collection of some of the most popular software currently being used in the analysis of next generation sequencing data.

License

Notifications You must be signed in to change notification settings

masoodzaka/bioinformatics_docker_app

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

32 Commits
 
 
 
 
 
 

Repository files navigation

Bioinformatics Docker App

Introduction

Software

Usage

Contributions and Updates

Introduction

This docker app is collection of some of the most popular software currently being used in the analysis of next generation sequencing data. All of the software are ready to use in the docker image that can be run on any machine (e.g. Mac, Linux and Windows) or on high performance cluster/computing platform via singularity. The docker app respository is available from the docker hub.

Software

Here is the list of software available through this docker app. All of the sotware binaries are paresent in the /opt directory and soft linked to the /usr/bin for ready to use. Each of the sotware/tool standard use or manual can be accessed on providers webpages.

Usage

Login account details for sudo


User: compbio

Password: bioinfo


For docker desktop (windows)

  • Pull image from online docker hub to local computer.
docker pull masoodzaka/bioinformatics:v1.0.0

  • Create a folder to map it to docker container on your window's drive
e.g. drive(d):/compbio

  • Start the your contianer using following command from the latest version of docker app
docker run -d -v d:/compbio:/home/compbio \
--name bioinfo_container \
-it masoodzaka/bioinformatics:<tag>
  • Connect to the running container using following command
docker exec -i -t bioinfo_container
  • Stop the running container
docker stop bioinfo_container
  • Re-running the existing will have two steps
docker start bioinfo_container 
docker attach bioinfo_container

For docker (Ubuntu)

  • Create a folder to map it to docker container using following command
sudo mkdir -p compbio

  • Start the your contianer using following command from the latest version of docker app
sudo docker run -d -v ~/compbio:/home/compbio \
--name bioinfo_container \
-it masoodzaka/bioinformatics:<tag>
  • Connect to the running container using following command
docker exec -i -t bioinfo_container

For HPC or Clusters

For security reasons, docker is not directory accessible on HPC or Computer clusters environment such as SGE or Slurm on private, research lab or University network. However, we can use Singularity such as this one from NIH as an ulternate for performing similar tasks. To learn more about singularity visit this documentation from Sylabs.

You can quick start singularity by pulling the docker image using following command.

singularity pull docker://masoodzaka/bioinformatics

Contributions and updates

Clone the main git repository using:

git clone https://github.com/masoodzaka/bioinformatics_docker_app.git

and make a new folder with version tag:

cd bioinformatics_docker_app
mkdir -p v1.0.1
cd v1.0.1
touch Dockerfile

Access the content of previous Dockerfile image using the "FROM" root container:

FROM masoodzaka/bioinformatics:v1.0.0

And build the latest docker image app using standard docker build command

docker build -t masoodzaka/bioinformatics:v1.0.1

Push the docker image

docker image push masoodzaka/bioinformatics:v1.0.1

The bioinformatics docker app will be regularly updated with latest software currently being implemented in the best practices analysis of high-throughput data.

About

This docker app is collection of some of the most popular software currently being used in the analysis of next generation sequencing data.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published