UNR-CFB/lahontan:latest
$ singularity pull shub://UNR-CFB/lahontan:latest
Singularity Recipe
Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
###############################################################
# Command used to build:
# sudo singularity build lahontan.simg Singularity
###############################################################
%labels
MAINTAINER Alberto Nava
VERSION v1.0
%post
locale-gen en_US.UTF-8
echo "Installing necessary packages..."
echo "deb http://us.archive.ubuntu.com/ubuntu/ xenial universe" >> /etc/apt/sources.list
apt-get update && apt-get install --yes git cmake gcc g++ libncurses-dev libhdf5-cpp-11 libhdf5-dev python3-docopt vim unzip openjdk-8-jdk-headless wget gfortran libbz2-dev liblzma-dev libpcre++-dev libcurl4-openssl-dev libssl-dev pandoc texlive-latex-extra libxml2-dev libmariadb-client-lgpl-dev libreadline6-dev libreadline6 libtbb-dev bzip2
cd /opt
wget https://cran.r-project.org/src/base/R-3/R-3.4.3.tar.gz
tar xzf R-3.4.3.tar.gz
cd R-3.4.3
./configure --with-x=no
make && make install
R -e 'source("https://bioconductor.org/biocLite.R");biocLite(ask=FALSE);biocLite(c("devtools","DESeq2","edgeR","ReportingTools","regionReport","pachterlab/sleuth","ballgown","DT","pheatmap"));devtools::install_github(c("docopt/docopt.R","alyssafrazee/RSkittleBrewer"))'
echo "Cloning repository..."
git clone --recursive https://github.com/UNR-CFB/lahontan.git /lahontan
echo "Installing pipeline..."
cd /lahontan
echo 'export RNASEQDIR=/lahontan/bin' >> $SINGULARITY_ENVIRONMENT
/lahontan/lib/autoSetup.sh
ln -s /usr/local/bin/R /lahontan/bin/R
ln -s /usr/local/bin/Rscript /lahontan/bin/Rscript
%environment
RNASEQDIR=/lahontan/bin
PATH="${PATH}:/lahontan/bin:/lahontan/lib"
LANG=en_US.UTF-8
LANGUAGE=en_US
export RNASEQDIR PATH LANG LANGUAGE
%help
Go to https://github.com/UNR-CFB/lahontan for more help OR try "./lahontan.simg -h" for pipeline help
%runscript
exec /lahontan/lib/lahontan "$@"
Collection
- Name: UNR-CFB/lahontan
- License: GNU General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/UNR-CFB-lahontan-latest |
collection name | UNR-CFB/lahontan |
branch | master |
tag | latest |
commit | eb0abdec585da93a12de8615fb216d838c2d5ddc |
version (container hash) | 108af69556c7ebff0047c9eb9757b4c0 |
build date | 2018-01-10T06:32:43.264Z |
size (MB) | 6102 |
size (bytes) | 3810979871 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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