onuryukselen/SignallingSingleCell_singularity:latest
$ singularity pull shub://onuryukselen/SignallingSingleCell_singularity:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:16.04
%labels
AUTHOR Onur Yukselen <onur.yukselen@umassmed.edu>
Version v1.0
%environment
PATH=$PATH:/bin:/sbin
export PATH
%post
apt-get update
apt-get -y upgrade
apt-get dist-upgrade
apt-get -y install unzip libsqlite3-dev libbz2-dev libssl-dev python python-dev \
python-pip git libxml2-dev software-properties-common wget tree vim \
subversion g++ gcc gfortran libcurl4-openssl-dev curl
###################
## Python modules
###################
export LC_ALL=C
pip install --upgrade pip==9.0.3
pip install pysam
pip install numpy scipy biopython
###################
## JAVA
###################
echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections && \
add-apt-repository -y ppa:webupd8team/java && \
apt-get update && \
apt-get install -y oracle-java8-installer && \
rm -rf /var/lib/apt/lists/* && \
rm -rf /var/cache/oracle-jdk8-installer
apt-get -y autoremove
###################
## NEXTFLOW
###################
export JAVA_HOME=/usr/lib/jvm/java-8-oracle
mkdir /data && cd /data
curl -s https://get.nextflow.io | bash
mv /data/nextflow /usr/bin/.
mkdir /project /nl /share /.nextflow
#################
## R ##
#################
NPROCS=`awk '/^processor/ {s+=1}; END{print s}' /proc/cpuinfo`
cd /tmp
wget http://security.ubuntu.com/ubuntu/pool/main/i/icu/libicu52_52.1-3ubuntu0.8_amd64.deb
dpkg -i libicu52_52.1-3ubuntu0.8_amd64.deb
wget https://cran.rstudio.com/src/base/R-3/R-3.5.1.tar.gz
tar xvf R-3.5.1.tar.gz
cd /tmp/R-3.5.1
apt-get update
apt-get install -y libblas3 libblas-dev liblapack-dev liblapack3 ghostscript libicu52
apt-get install -y libgmp10 libgmp-dev
apt-get install -y fort77 aptitude
aptitude install -y xorg-dev
aptitude install -y libreadline-dev
apt install -y libpcre3-dev liblzma-dev
apt-get update
apt-get install -y bioperl
apt-get update
./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes
echo "Will use make with $NPROCS cores."
make -j${NPROCS}
make install
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite()"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('scran')"
echo install.packages\(\"devtools\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
yes | apt-get install libmariadb-client-lgpl-dev
R --slave -e "library(devtools); devtools::install_github('davismcc/scater', build_vignettes = TRUE)"
echo install.packages\(\"rmarkdown\"\, dependencies = TRUE, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('scater')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('BiocStyle')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('destiny')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('mvoutlier')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('mvoutlier')"
R --slave -e "library(devtools); install_github('garber-lab/SignallingSingleCell')"
R --slave -e "library('SignallingSingleCell')"
R --slave -e "library('SingleCellExperiment')"
Collection
- Name: onuryukselen/SignallingSingleCell_singularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/onuryukselen-SignallingSingleCell_singularity-latest |
collection name | onuryukselen/SignallingSingleCell_singularity |
branch | master |
tag | latest |
commit | 81689462fd4665457fd873340b8921570ee354e7 |
version (container hash) | 262b2a0c0b8a9a59132b578a323b50ab |
build date | 2018-07-29T13:44:02.861Z |
size (MB) | 3494 |
size (bytes) | 1247858719 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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