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GoSTRIPES.def
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bootstrap: docker
From: ubuntu:20.04
%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-dev-compat
apt -y install libpq-dev
apt -y install libssl-dev
apt -y install libtbb-dev
apt -y install libxml2-dev
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_v0.11.9.zip
unzip fastqc_v0.11.9.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/0.6.7.zip
mv 0.6.7.zip TrimGalore-0.6.7.zip
unzip TrimGalore-0.6.7.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*
\rm *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/3.0.1/sratoolkit.3.0.1-ubuntu64.tar.gz
tar -xzf sratoolkit.3.0.1-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 http://github.com/samtools/htslib.git htslib
cd htslib
git submodule update --init --recursive
make && make install && make clean
echo 'Installing SAMTOOLS from http://www.htslib.org/ '
#### Prerequisites
apt -y install ncurses-dev
#### Install
cd /opt
git clone http://github.com/samtools/samtools.git samtools
cd samtools
make && make install && make clean
### 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-1.6.2.tar.gz
tar -xzf genometools-1.6.2.tar.gz
cd genometools-1.6.2/
make && make install
echo 'Installing bedtools from https://github.com/arq5x/bedtools2/ '
cd /opt
git clone https://github.com/arq5x/bedtools2.git
cd bedtools2/
make && make install && make clean
echo 'Installing bedops from https://github.com/bedops '
cd /opt
mkdir bedops && cd bedops
wget https://github.com/bedops/bedops/releases/download/v2.4.40/bedops_linux_x86_64-v2.4.40.tar.bz2
tar jxvf bedops_linux_x86_64-v2.4.40.tar.bz2
# ... creates bin directory with tool binaries; added to path below
\rm bedops_linux_x86_64-v2.4.40.tar.bz2
echo 'Installing gfftobed from https://github.com/jacobbierstedt/gfftobed.git '
cd /opt
git clone https://github.com/jacobbierstedt/gfftobed.git
cd gfftobed
make
cp gfftobed /usr/local/bin
### All things R
echo 'Installing R'
####
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
apt -y update
apt -y install r-base
R CMD javareconf
echo 'Installing CRAN and Bioconductor packages'
######
echo 'install.packages("BiocManager", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' > R2install
echo 'BiocManager::install(c("BiocVersion"), ask=FALSE)' >> R2install
echo 'install.packages("dplyr", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("gplots", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("ggplot2", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("ggdendro", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("gtable", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("gridExtra", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("pastecs", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("RCurl", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("rJava", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("shiny", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("sqldf", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("tidyr", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("venneuler", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("XML", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' >> R2install
echo 'install.packages("R.devices", repos="http://ftp.ussg.iu.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 https://github.com/BrendelGroup/GoSTRIPES '
#### Install
cd /opt
git clone https://github.com/BrendelGroup/GoSTRIPES
%environment
export LC_ALL=C
export PATH=$PATH:/opt/bedops/bin
export PATH=$PATH:/opt/FastQC
export PATH=$PATH:/opt/GoSTRIPES/bin
export PATH=$PATH:/opt/hisat2
export PATH=$PATH:/opt/sratoolkit.3.0.1-ubuntu64/bin
export PATH=$PATH:/opt/STAR/bin/Linux_x86_64
export PATH=$PATH:/opt/TrimGalore-0.6.7
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/
%labels
Maintainer vpbrendel
Version v1.2