BrendelGroup/BWASP:latest
$ singularity pull shub://BrendelGroup/BWASP:latest
Singularity Recipe
bootstrap: docker
From: ubuntu:20.04
%help
This container provides portable & reproducible components for BWASP:
Bisulfite-seq data Workflow Automation Software and Protocols from the Brendel Group.
Please see https://github.com/BrendelGroup/BWASP for complete documentation.
%post
export DEBIAN_FRONTEND=noninteractive
apt -y update
apt -y install bc git pigz tcsh unar unzip zip wget tzdata \
build-essential \
openjdk-11-jre-headless \
python3-pip python3-pycurl python3-yaml python3-pandas \
cpanminus
# Make sure "python" is found:
ln -s /usr/bin/python3 /usr/bin/python
echo 'Installing HTSLIB from http://www.htslib.org/ '
#### Prerequisites
apt -y install libcurl4-openssl-dev zlib1g-dev libbz2-dev liblzma-dev
#### Install
cd /opt
git clone git://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 git://github.com/samtools/samtools.git samtools
cd samtools
make && make install && make clean
echo 'Installing Bowtie2 from https://github.com/BenLangmead/bowtie2 '
######
cd /opt
wget --content-disposition https://github.com/BenLangmead/bowtie2/releases/download/v2.3.5.1/bowtie2-2.3.5.1-linux-x86_64.zip
unzip bowtie2-2.3.5.1-linux-x86_64.zip
echo 'Installing BISMARK from http://www.bioinformatics.babraham.ac.uk/projects/bismark/ '
#### Prerequisites
apt -y install libgd-dev libgd-graph-perl
#####
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_v0.11.8.zip
unzip fastqc_v0.11.8.zip
chmod +x FastQC/fastqc
echo 'Installing SRA Toolkit from https://github.com/ncbi/sra-tools '
######
cd /opt
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.7/sratoolkit.2.10.7-ubuntu64.tar.gz
tar -xzf sratoolkit.2.10.7-ubuntu64.tar.gz
echo 'Installing TRIM_GALORE from http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ '
#### Prerequisites
pip3 install cutadapt
#### Install
cd /opt
wget --content-disposition https://github.com/FelixKrueger/TrimGalore/archive/0.6.3.zip
unzip TrimGalore-0.6.3.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-1.6.1.tar.gz
tar -xzf genometools-1.6.1.tar.gz
cd genometools-1.6.1/
make && make install && make clean
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 AEGeAn from https://github.com/BrendelGroup/AEGeAn/ '
######
cd /opt
git clone https://github.com/BrendelGroup/AEGeAn.git
cd AEGeAn/
make && make install && make clean
echo 'Installing BWASP from https://github.com/BrendelGroup/BWASP.git '
#### Prerequisites
apt -y install python3-numpy python3-scipy
cpanm Getopt::Long Math::BigFloat Array::Split Parallel::Loops
#### Install
cd /opt
git clone https://github.com/BrendelGroup/BWASP.git
%environment
export LC_ALL=C
export PATH=$PATH:/opt/bowtie2-2.3.5.1-linux-x86_64
export PATH=$PATH:/opt/Bismark
export PATH=$PATH:/opt/FastQC
export PATH=$PATH:/opt/sratoolkit.2.10.7-ubuntu64/bin
export PATH=$PATH:/opt/TrimGalore-0.6.3
export PATH=$PATH:/opt/BWASP/bin
export PATH=$PATH:/opt/aspera/cli/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/
%labels
Maintainer vpbrendel
Version v1.0
Collection
- Name: BrendelGroup/BWASP
- License: GNU General Public License v2.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/BrendelGroup-BWASP-latest |
collection name | BrendelGroup/BWASP |
branch | master |
tag | latest |
commit | 3e6df2ef5ab6450e52f03cb9ff4f1beb5a9bbff1 |
version (container hash) | 7f78cc2749326c3589029a717e1594eb |
build date | 2021-04-09T20:13:23.687Z |
size (MB) | 2319.0 |
size (bytes) | 1029160991 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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