bootstrap: docker From: ubuntu:18.04 %help This container provides portable & reproducible components for GoSTRIPES: Workflows for STRIPE-seq data analysis (from Brendel Group). Please see https://github.com/BrendelGroup/GoSTRIPES for complete documentation. %post export DEBIAN_FRONTEND=noninteractive 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 cython cython3 apt -y install openjdk-8-jdk apt -y install software-properties-common apt -y install libbz2-dev apt -y install libcairo2-dev apt -y install libcurl4-openssl-dev apt -y install libcurl4-gnutls-dev apt -y install libudunits2-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 ### Read quality control 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_v0.11.8.zip unzip fastqc_v0.11.8.zip chmod +x FastQC/fastqc echo 'Installing TRIM_GALORE from http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ' #### Prerequisites pip3 install --upgrade cutadapt #### Install cd /opt wget https://github.com/FelixKrueger/TrimGalore/archive/0.6.4.zip mv 0.6.4.zip TrimGalore-0.6.4.zip unzip TrimGalore-0.6.4.zip echo 'Installing Trimmomatic from http://www.usadellab.org/cms/index.php?page=trimmomatic ' #### Install cd /opt wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip unzip Trimmomatic-0.39.zip # Use: java -jar /opt/Trimmomatic-0.39/trimmomatic-0.39.jar echo 'Installing TagDust from https://sourceforge.net/projects/tagdust/files/latest/download ' #### Install cd /opt wget --content-disposition https://sourceforge.net/projects/tagdust/files/tagdust-2.33.tar.gz/download tar -xzf tagdust-2.33.tar.gz cd tagdust-2.33/ ./configure make make install ### Read manipulation echo 'Installing SRATOOLKIT from http://www.ncbi.nlm.nih.gov/books/NBK158900/ ' ###### Install cd /opt wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.5/sratoolkit.2.10.5-ubuntu64.tar.gz tar -xzf sratoolkit.2.10.5-ubuntu64.tar.gz echo 'Installing UMI-tools from https://github.com/CGATOxford/UMI-tools ' #### Install pip3 install --upgrade umi-tools ### Read mapping echo 'Installing bwa from https://github.com/lh3/bwa ' ###### Install cd /opt git clone https://github.com/lh3/bwa.git cd bwa make cp bwa /usr/local/bin/ echo 'Installing BOWTIE2 from http://bowtie-bio.sourceforge.net/bowtie2 ' ###### Install apt -y install bowtie2 echo 'Installing hisat2 from https://ccb.jhu.edu/software/hisat2/ ' ###### Install cd /opt git clone https://github.com/infphilo/hisat2 hisat2 cd hisat2 make echo 'Installing STAR from https://github.com/alexdobin/STAR ' ###### Install cd /opt git clone https://github.com/alexdobin/STAR ### Alignment utilities 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 ### Genome utilities 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 ### All things R 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-biocmanager apt -y install r-cran-dplyr apt -y install r-cran-ggplot2 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-tidyr 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://mirror.las.iastate.edu/CRAN/", dependencies=TRUE)' > R2install echo 'BiocManager::install(c("BiocGenerics", "GenomicRanges", "genomation", "TSRchitect"),ask=FALSE)' >> R2install echo 'BiocManager::install(c("bumphunter", "seqLogo", "ENCODExplorer", "edgeR"),ask=FALSE)' >> R2install echo 'BiocManager::install(c("ChIPseeker", "ChIPpeakAnno"),ask=FALSE)' >> R2install echo 'BiocManager::install(c("TxDb.Scerevisiae.UCSC.sacCer3.sgdGene", "org.Sc.sgd.db"),ask=FALSE)' >> R2install Rscript R2install ### Tools to analyze mapped reads echo 'Installing RSEM from http://deweylab.github.io/RSEM/ ' #### Install cd /opt git clone https://github.com/deweylab/RSEM.git cd RSEM make make ebseq make install echo 'Installing GoSTRIPES from git://github.com/BrendelGroup/GoSTRIPES ' #### Install cd /opt git clone git://github.com/BrendelGroup/GoSTRIPES %environment export LC_ALL=C export PATH=$PATH:/opt/FastQC export PATH=$PATH:/opt/GoSTRIPES/bin export PATH=$PATH:/opt/hisat2 export PATH=$PATH:/opt/sratoolkit.2.10.5-ubuntu64/bin export PATH=$PATH:/opt/STAR/bin/Linux_x86_64 export PATH=$PATH:/opt/TrimGalore-0.6.4 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/ %labels Maintainer vpbrendel Version v1.1