I. What is this?

Reproducible bioinformatics workspace with docker under Centos7.

II. How to use it?

II.1/ Requirements

* Docker: https://docs.docker.com

II.2/ Usage

a) From the image

docker pull najlabioinfo/najlabioinfospace

b) From the Dockerfile

docker build --tag="yourTag" --file="/pathto/Dockerfile"

* Dockerfile sample

############################################################ 
# Dockerfile based on Centos Image 
############################################################ 
# Set the base image to use to Centos
FROM centos:7
# Set the file maintainer (your name - the file's author) 
MAINTAINER "Najla BEN HASSSINE" bhndevtools@gmail.com
#Prepare env and extra-package install
RUN yum install -y sudo epel-release-7-5.noarch.rpm deltarpm
#MAKE PATH SHAR
RUN mkdir -p /usr/share/info
RUN useradd najlabioinfo \
    && chown najlabioinfo:najlabioinfo /home/najlabioinfo
#Install devtools
RUN yum -y groupinstall "Development Tools"  
RUN yum -y install curl git irb m4 ruby texinfo bzip2-devel curl-devel expat-devel ncurses-devel zlib-devel ghostscript wget cmake git github-backup pandoc gcc g++ kernel-devel htop kpathsea which latex web2c dvips libRmath-devel libRmath zip libreadline-dev readline-devel libreadline pdftailor pdftk mozilla tiff2pdf qpdf xpdf evince which gcc-c++ cairo-devel libpng-devel libX11 libX11-devel qt libjpeg-turbo java info xorg-x11-server-Xvfb firefox texlive
#Needed package for R
RUN yum -y groupinstall X11
RUN yum install -y  libXt-dev libgtk2.0-dev libcairo2-dev xvfb xauth xfonts-base zip libreadline-dev readline-devel libreadline pdftailor pdftk mozilla tiff2pdf texlive qpdf xpdf evince which pdftohtml texinfo inconsolata-fonts
#Updating package
RUN yum update -y
#Install Dev packages
RUN yum install -y  curl gcc make perl git perl-devel expat-devel zlib-devel libbamtools links pdftohtml
#METHODE A : Sample
#-INSTALL firepony
RUN curl -o /etc/yum.repos.d/packages.shadau.com.repo \
    http://packages.shadau.com/rpm/centos-7/packages.shadau.com.repo
RUN yum install -y firepony

>> Message success build: Successfully built ID_CONTAINER

c) Upgrading

II.3/ Running

docker run -it najlabioinfo/najlabioinfospace R

fastqc

docker run -it najlabioinfo/najlabioinfospace fastqc --help

docker run -ti najlabioinfo/najlabioinfospace bwa meme

bowtie2

docker run -it najlabioinfo/najlabioinfospace bowtie2 --help

III. Resources

III.1/ Documentation

A comprehensive documentation for docker library is here: https://github.com/docker-library/docs

If you have doubt on how to use Docker, please visit the Docker website : https://docs.docker.com/engine/reference/builder/

III.2/ References

(ubuntu:14.04.3): Biodocker project: https://github.com/BioDocker/biodocker
(Debian): Moreews F, Sallou O, Ménager H et al. BioShaDock: a community driven bioinformatics shared Docker-based tools registry [version 1; referees: 2 approved]. F1000Research 2015, 4:1443 (doi: 10.12688/f1000research.7536.1)
(Scientific Linux 6.5): Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C. The impact of Docker containers on the performance of genomic pipelines. Campagne F, ed. PeerJ. 2015;3:e1273. doi:10.7717/peerj.1273.
(R): Launch R directly for interactive work here https://hub.docker.com/_/r-base

IV. Issues and Contributing

IV.1/ Support

If you are having issues, please let me know.

IV.2/ Contribute

Bug reports, bug fixes, and new features are always welcome.
* Issue Tracker: github
* Source Code: github

IV.3/ Authors and Maintainers

BEN HASSINE NAJLA : bhndevtools@gmail.com

DockerBIum

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