bootstrap: docker From: ubuntu:18.04 %help This container provides portable & reproducible components for BWASP: Bisulfite-seq data Workflow Automation Software and Protocols from Brendel Group. Please see https://github.com/BrendelGroup/BWASP for complete documentation. %post apt -y update apt -y install build-essential apt -y install bc git tcsh tzdata unzip zip wget apt -y install cpanminus apt -y install openjdk-8-jdk apt -y install software-properties-common apt -y install libcurl4-openssl-dev apt -y install libcurl4-gnutls-dev apt -y install libgd-dev apt -y install libmariadb-client-lgpl-dev apt -y install libpq-dev apt -y install libssl-dev apt -y install libtbb-dev apt -y install libxml2-dev apt -y install python-minimal apt -y install python-pip apt -y install python3-minimal apt -y install python3-pip echo 'Installing HTSLIB from http://www.htslib.org/ ' #### Prerequisites apt -y install zlib1g-dev libbz2-dev liblzma-dev #### Install cd /opt git clone git://github.com/samtools/htslib.git htslib cd htslib make && make install echo 'Installing SAMTOOLS from http://www.htslib.org/ ' #### Prerequisites apt -y install ncurses-dev #### Install cd /opt git clone git://github.com/samtools/samtools.git samtools cd samtools make && make install echo 'Installing BOWTIE2 from http://bowtie-bio.sourceforge.net/bowtie2 ' ###### apt -y install bowtie2 echo 'Installing BISMARK from http://www.bioinformatics.babraham.ac.uk/projects/bismark/ ' ###### cd /opt git clone https://github.com/BrendelGroup/Bismark # Note that we are using the slightly modified Brendel Group version of Bismark echo 'Installing FASTQC from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ' #### Install cd /opt wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip unzip fastqc_v0.11.5.zip chmod +x FastQC/fastqc echo 'Installing SRATOOLKIT from http://www.ncbi.nlm.nih.gov/books/NBK158900/ ' ###### cd /opt wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2/sratoolkit.2.8.2-ubuntu64.tar.gz tar -xzf sratoolkit.2.8.2-ubuntu64.tar.gz echo 'Installing TRIM_GALORE from http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ' #### Prerequisites pip install --upgrade cutadapt #### Install cd /opt wget http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v0.4.1.zip unzip trim_galore_v0.4.1.zip echo 'Installing GENOMETOOLS from from http://genometools.org/ ' #### Prerequisites apt -y install libcairo2-dev libpango1.0-dev #### Install cd /opt wget http://genometools.org/pub/genometools-1.5.10.tar.gz tar -xzf genometools-1.5.10.tar.gz cd genometools-1.5.10/ make && make install echo 'Installing AEGeAn from https://github.com/BrendelGroup/AEGeAn/ ' ###### cd /opt git clone https://github.com/BrendelGroup/AEGeAn.git cd AEGeAn/ make && make install echo 'Installing BWASP from https://github.com/BrendelGroup/BWASP.git ' #### Prerequisites apt -y install python-numpy python-scipy cpanm --configure-timeout 3600 GD::Graph::lines cpanm --configure-timeout 3600 LWP::UserAgent cpanm --configure-timeout 3600 Math::Pari #### Install cd /opt git clone https://github.com/BrendelGroup/BWASP.git echo 'Installing R' #### export DEBIAN_FRONTEND=noninteractive add-apt-repository -y ppa:marutter/rrutter3.5 add-apt-repository -y ppa:marutter/c2d4u3.5 apt -y update apt -y install r-base-core r-base-dev R CMD javareconf echo 'Installing CRAN packages' ###### apt -y install r-cran-dplyr apt -y install r-cran-gplots apt -y install r-cran-gridextra apt -y install r-cran-pastecs apt -y install r-cran-rjava apt -y install r-cran-sqldf apt -y install r-cran-venneuler apt -y install r-cran-rcurl apt -y install r-cran-xml2 echo 'Installing other CRAN and Bioconductor packages' ###### echo 'install.packages("R.devices", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' > R2install echo 'source("https://bioconductor.org/biocLite.R")' >> R2install echo 'biocLite(c("BiocGenerics", "GenomicRanges", "genomation","methylKit"),ask=FALSE)' >> R2install Rscript R2install echo 'Installing BWASPR from https://github.com/BrendelGroup/BWASPR/ ' ###### cd /opt git clone https://github.com/BrendelGroup/BWASPR.git R CMD INSTALL BWASPR %environment export LC_ALL=C export PATH=$PATH:/opt/Bismark export PATH=$PATH:/opt/FastQC export PATH=$PATH:/opt/sratoolkit.2.8.2-ubuntu64/bin export PATH=$PATH:/opt/trim_galore_zip export PATH=$PATH:/opt/BWASP/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/ %labels Maintainer vpbrendel Version v0.9