BrendelGroup/GoSTRIPES:latest
$ singularity pull shub://BrendelGroup/GoSTRIPES:latest
Singularity Recipe
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
Collection
- Name: BrendelGroup/GoSTRIPES
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/BrendelGroup-GoSTRIPES-latest |
collection name | BrendelGroup/GoSTRIPES |
branch | master |
tag | latest |
commit | eaff2ad79b3368f93a7aad552a26698bd2b8d75b |
version (container hash) | 8fe785d9a7822a46cc2b604debf9e207 |
build date | 2021-04-01T19:12:01.597Z |
size (MB) | 4386.0 |
size (bytes) | 2128912415 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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