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TSRchitect.def
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bootstrap: docker
From: ubuntu:22.04
%help
This container provides portable & reproducible components for TSRchitect,
including upstream components for read quality control and mapping.
%post
export DEBIAN_FRONTEND=noninteractive
apt -y update
apt -y install build-essential
apt -y install bc curl git tcsh unzip zip wget
apt -y install automake cmake
apt -y install cpanminus
apt -y install cython3
apt -y install openjdk-11-jdk ant
apt -y install software-properties-common
apt -y install zlib1g-dev libbz2-dev liblzma-dev
apt -y install libcairo2-dev libpango1.0-dev
apt -y install libcurl4-openssl-dev
apt -y install libcurl4-gnutls-dev
apt -y install libgd-dev
apt -y install libgdal-dev
apt -y install libgtextutils-dev
apt -y install libncurses-dev
apt -y install libpq-dev
apt -y install libproj-dev
apt -y install libsodium-dev
apt -y install libssl-dev
apt -y install libtool
apt -y install libtbb-dev
apt -y install libudunits2-dev
apt -y install libxml2-dev
apt -y install libbz2-dev
apt -y install m4
apt -y install parallel
apt -y install python2-minimal python-is-python3
apt -y install python3-minimal
apt -y install python3-pip
apt -y install openmpi-bin openmpi-common openssh-client openssh-server
apt -y install libopenmpi-dev
cd /opt
mkdir bin
###
# Utilities
#
apt -y install python3-numpy python3-scipy
pip3 install --upgrade dinopy HTSeq
# genometools:
#
echo 'Installing GENOMETOOLS from from http://genometools.org/ '
cd /opt
wget http://genometools.org/pub/genometools-1.6.2.tar.gz
tar -xzf genometools-1.6.2.tar.gz
cd genometools-1.6.2/
make && make install
cd ..
# fastq-multx:
#
echo 'Installing fastx_multx from https://github.com/brwnj/fastq-multx.git '
git clone https://github.com/brwnj/fastq-multx.git
cd fastq-multx/
make
cp fastq-multx /usr/local/bin/
cd ..
# fastx_toolkit:
#
echo 'Installing fastx_toolkit from https://github.com/agordon/fastx_toolkit.git '
git clone https://github.com/agordon/fastx_toolkit.git
cd fastx_toolkit/
sed -i -e "s/usage();$/usage();exit(1);/" src/fasta_formatter/fasta_formatter.cpp
./reconf
./configure
make
make install
cd ..
# SAMTOOLS:
#
echo 'Installing htslib from http://www.htslib.org/ '
git clone https://github.com/samtools/htslib.git
cd htslib
make && make install
cd ..
echo 'Installing samtools from http://www.htslib.org/ '
git clone https://github.com/samtools/samtools.git
cd samtools
make && make install
cd ..
# NGSUtils:
#
echo 'Installing ngsutilsj from https://github.com/compgen-io/ngsutilsj.git '
git clone https://github.com/compgen-io/ngsutilsj
cd ngsutilsj
ant jar
ln -s /opt/ngsutilsj/dist/ngsutilsj /usr/local/bin/ngsutilsj
cd ../..
# SRATOOLKIT:
#
echo 'Installing SRATOOLKIT from https://www.ncbi.nlm.nih.gov/books/NBK158900/ '
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.1/sratoolkit.3.0.1-ubuntu64.tar.gz
tar -xzf sratoolkit.3.0.1-ubuntu64.tar.gz
###
# Evaluation and trimming of reads:
#
# FASTQC:
#
echo 'Installing FASTQC from https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ '
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
unzip fastqc_v0.11.9.zip
chmod a+x FastQC/fastqc
# TRIM_GALORE:
echo 'Installing TRIM_GALORE from http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ '
#### Prerequisites
pip install --upgrade cutadapt
### Install
wget --content-disposition https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.zip
unzip TrimGalore-0.6.6.zip
cp TrimGalore-0.6.6/trim_galore /opt/bin
# TagDust:
#
echo 'Installing TagDust from https://sourceforge.net/projects/tagdust/files/latest/download '
mkdir TagDust
cd TagDust
wget --content-disposition https://sourceforge.net/projects/tagdust/files/tagdust-2.33.tar.gz/download
tar -xzf tagdust-2.33.tar.gz*
\rm tagdust-2.33.tar.gz*
cd tagdust-2.33/
./configure CFLAGS=-fcommon
make
make install
cd ../..
# TRIMMOMATIC:
#
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
###
# Read mapping tools:
#
# BOWTIE:
apt -y install bowtie
# BOWTIE2:
apt -y install bowtie2
# BWA:
echo 'Installing bwa from https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2/download '
wget --content-disposition https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2/download
tar -xjf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
sed -i -e "s/CFLAGS= -g -Wall -Wno-unused-function -O2/CFLAGS= -g -Wall -Wno-unused-function -O2 -fcommon/" Makefile
make
cp bwa /opt/bin/
cd ../
# HISAT2:
echo 'Installing hisat2 from https://github.com/DaehwanKimLab/hisat2 '
wget https://github.com/DaehwanKimLab/hisat2/archive/refs/tags/v2.2.1.tar.gz
tar -xzf v2.2.1.tar.gz
cd hisat2-2.2.1
make
cd ../
# STAR:
echo 'Installing STAR from https://github.com/alexdobin/STAR '
git clone https://github.com/alexdobin/STAR.git
cd STAR
cd source
make STAR
cp STAR /opt/bin
cd ../..
###
# Spliced alignment tools:
#
echo 'Installing GeneSeqer spliced aligner from https://github.com/BrendelGroup/GeneSeqer '
git clone https://github.com/BrendelGroup/GeneSeqer.git
cd GeneSeqer/src
make linux
make clean
cp makefile.lnxMPI makefile.lnxMPIorig
sed -e "s/^#MPICC/MPICC/" makefile.lnxMPI | sed -e "0,/^MPICC/s/^MPICC/#MPICC/" > makefile.lnxMPIu
make -f makefile.lnxMPIu
make clean
make install
cd ../..
###
# Motif identification:
#
# GHOSTSCRIPT:
#
echo 'Installing ghostscript from https://ghostscript.readthedocs.io/en/gs10.0.0/ '
wget https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs1000/ghostpcl-10.0.0-linux-x86_64.tgz
tar -xzf ghostpcl-10.0.0-linux-x86_64.tgz
cd ghostpcl-10.0.0-linux-x86_64
chmod a+x gpcl6-1000-linux-x86_64
cp gpcl6-1000-linux-x86_64 /opt/bin/gs
cd ../
# MEME:
#
echo 'Installing meme from https://meme-suite.org/meme/ '
wget https://meme-suite.org/meme/meme-software/5.5.0/meme-5.5.0.tar.gz
tar -xzf meme-5.5.0.tar.gz
cd meme-5.5.0
./configure --prefix=/opt/meme \
--enable-build-libxml2 --enable-build-libxslt --with-url="http://meme-suite.org"
make
# make test
make install
cd ../
# WEBLOGO:
#
echo 'Installing weblogo from https://weblogo.berkeley.edu/ '
wget https://weblogo.berkeley.edu/release/weblogo.2.8.2.tar.gz
tar -xzf weblogo.2.8.2.tar.gz
# HOMER:
echo 'Installing home from http://homer.salk.edu/homer/ '
mkdir HOMER; cd HOMER
wget http://homer.salk.edu/homer/configureHomer.pl
cpanm HTML::Template
cpanm JSON
cpanm XML::Simple
cpanm XML::Compile::SOAP11
cpanm XML::Compile::WSDL11
cpanm XML::Compile::Transport::SOAPHTTP
cpanm Log::Log4perl
cpanm Math::CDF
pip install --upgrade networkx
perl configureHomer.pl -install homer
chmod -R a+w data
cd ../
###
# R and R packages, including TSRchitect
#
apt -y update -qq
apt install --no-install-recommends software-properties-common dirmngr
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt -y install --no-install-recommends r-base-core r-base-dev
R CMD javareconf
echo 'Installing CRAN packages'
######
apt -y install r-cran-biocmanager
apt -y install r-bioc-annotationhub
apt -y install r-bioc-biocgenerics
apt -y install r-bioc-genomicranges
apt -y install r-bioc-biocversion
apt -y install r-cran-dplyr
apt -y install r-cran-gplots
apt -y install r-cran-gridextra
apt -y install r-cran-sqldf
apt -y install r-cran-rcurl
apt -y install r-cran-readxl
apt -y install r-cran-statmod
apt -y install r-cran-xml2
echo 'Installing other CRAN and Bioconductor packages'
######
echo 'install.packages(c("pastecs", "venneuler"), repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' > R2install
echo 'BiocManager::install(version = "3.16", ask=FALSE)' >> R2install
echo 'BiocManager::install(c("genomation","TSRchitect"), ask=FALSE)' >> R2install
echo 'BiocManager::install(c("bumphunter","seqLogo","ENCODExplorerData"), ask=FALSE)' >> R2install
echo 'BiocManager::install(c("edgeR","R2HTML"), ask=FALSE)' >> R2install
Rscript R2install
# Install the last working version of ENCODExplorer (no 3.16 version is currently available):
#
wget https://bioconductor.org/packages/3.12/bioc/src/contrib/ENCODExplorer_2.16.0.tar.gz
tar -xzf ENCODExplorer_2.16.0.tar.gz
R CMD INSTALL ENCODExplorer
# Use the git repository for installation of a TSRchitect version not yet in Bioconductor:
#
git clone https://github.com/vpbrendel/TSRchitect.git
R CMD INSTALL TSRchitect
%environment
export LC_ALL=C
export PATH=$PATH:/opt/bin
export PATH=$PATH:/opt/FastQC
export PATH=$PATH:/opt/hisat2-2.2.1
export PATH=$PATH:/opt/HOMER/bin
export PATH=$PATH:/opt/meme/bin
export PATH=$PATH:/opt/sratoolkit.3.0.1-ubuntu64/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/:/usr/lib64/openmpi/lib
%labels
Maintainer vpbrendel
Version v1.1