BrendelGroup/BWASPR:latest
$ singularity pull shub://BrendelGroup/BWASPR:latest
Singularity Recipe
bootstrap: docker
From: ubuntu:20.04
%help
This container is a companion to BWASP: Bisulfite-seq data Workflow Automation
Software and Protocols from the Brendel Group, providing R packages and scripts
for BWASP data analyses.
Please see https://github.com/BrendelGroup/BWASPR for complete documentation.
%post
export DEBIAN_FRONTEND=noninteractive
apt -y update
apt-get -y upgrade
apt -y install bc bzip2 git tcsh tzdata unzip zip wget \
build-essential \
openjdk-11-jdk \
software-properties-common \
libcairo2-dev \
libcurl4-gnutls-dev \
libgd-dev \
libgd-graph-perl \
libmariadb-client-lgpl-dev-compat \
libpq-dev \
libssl-dev \
libtbb-dev \
libxml2-dev \
poppler-utils unoconv
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 '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("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("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("sqldf", 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","methylKit"), ask=FALSE)' >> R2install
Rscript R2install
echo 'Installing BWASPR from https://github.com/BrendelGroup/BWASPR '
######
cd /opt
git clone https://github.com/BrendelGroup/BWASPR.git
R CMD INSTALL BWASPR
echo 'Installing unoconv from https://github.com/unoconv/unoconv/archive/0.9.0.tar.gz '
######
cd /opt
wget https://github.com/unoconv/unoconv/archive/0.9.0.tar.gz
tar -xzf 0.9.0.tar.gz
sed -e "s#/usr/bin/env python#/usr/bin/env python3#" unoconv-0.9.0/unoconv > /usr/bin/unoconv
echo 'Installing rbo from https://github.com/dlukes/rbo '
######
cd /opt
git clone https://github.com/dlukes/rbo
%environment
export LC_ALL=C
export PATH=$PATH:/opt/BWASPR/bin
%labels
Maintainer vpbrendel
Version v1.1
Collection
- Name: BrendelGroup/BWASPR
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/BrendelGroup-BWASPR-latest |
collection name | BrendelGroup/BWASPR |
branch | master |
tag | latest |
commit | 725db571e6f426c6651089ecc00a9e27fb02b57c |
version (container hash) | 5537fafbf0d47ba240fd66a1557703fb |
build date | 2021-03-08T17:55:51.157Z |
size (MB) | 2283.0 |
size (bytes) | 1005314079 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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