motroy/singularity-minion-qc-tools:latest
$ singularity pull shub://motroy/singularity-minion-qc-tools:latest
Singularity Recipe
Bootstrap: docker
From: ubuntu:16.04
%labels
Maintainer motroy
%help
This container runs minion QC
%environment
export PATH=/opt/miniconda3/bin:/minion_qc/:$PATH
export OMPI_MCA_opal_cuda_support=true
%runscript
eval "$(conda shell.bash hook)"
source /opt/miniconda3/etc/profile.d/conda.sh
#conda activate pangolin
#exec qiime "${@}"
%post
# default mount points
mkdir -p /scratch/global /scratch/local /rcc/stor1/refdata /rcc/stor1/projects /rcc/stor1/depts
# Install necessary packages
apt-get update && apt-get install -y --no-install-recommends \
build-essential \
gcc-multilib \
ca-certificates \
locales \
git \
libjpeg62 \
curl wget less locate openssh-server zlib1g-dev libboost-all-dev \
perl libmoo-perl liblist-moreutils-perl libjson-perl fastqc pkg-config \
libfreetype6-dev libpng-dev python-matplotlib #python3 python3-numpy python3-scipy python3-pip
apt-get clean
echo "LC_ALL=en_US.UTF-8" >> /etc/environment
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
echo "LANG=en_US.UTF-8" > /etc/locale.conf
locale-gen en_US.UTF-8
# Install miniconda
wget https://repo.continuum.io/miniconda/Miniconda3-4.7.12.1-Linux-x86_64.sh -O miniconda3.sh
bash miniconda3.sh -b -p /opt/miniconda3
rm miniconda3.sh
export PATH="/opt/miniconda3/bin:$PATH"
export OMPI_MCA_opal_cuda_support=true
conda config --file /.condarc --add channels defaults && conda config --file /.condarc --add channels conda-forge && conda config --file /.condarc --add channels r && conda config --file /.condarc --add channels aleg
conda install -c anaconda yaml
conda install -c conda-forge r-base r-futile.logger r-optparse r-readr r-viridis
conda install -c r r-data.table r-dplyr r-ggplot2 r-reshape2 r-scales r-ggplot2 r-yaml
conda install -c aleg pycoqc
mkdir /minion_qc
wget "https://github.com/roblanf/minion_qc/releases/download/1.4.2/MinIONQC.R" -O /minion_qc/MinIONQC-1.4.2.R
export PATH="/minion_qc/:$PATH"
Collection
- Name: motroy/singularity-minion-qc-tools
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/motroy-singularity-minion-qc-tools-latest |
collection name | motroy/singularity-minion-qc-tools |
branch | master |
tag | latest |
commit | 6d9bdcce8dc3363ebff58c06bdfe4fb31b4f7362 |
version (container hash) | f0f6ac2f3321355decca297234d1320f |
build date | 2020-08-23T11:54:27.530Z |
size (MB) | 3631.0 |
size (bytes) | 1607970847 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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