jdwheaton/singularity-ngs:hicpro
$ singularity pull shub://jdwheaton/singularity-ngs:hicpro
Singularity Recipe
Bootstrap: docker
From: ubuntu:xenial
%labels
AUTHOR Nicolas Servant
%post
apt-get update
apt-get install -y wget
apt-get install -y gzip
apt-get install -y bzip2
apt-get install -y curl
apt-get install -y unzip
## g++
apt-get install -y build-essential
# install anaconda
if [ ! -d /usr/local/anaconda ]; then
wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh \
-O ~/anaconda.sh && \
bash ~/anaconda.sh -b -p /usr/local/anaconda && \
rm ~/anaconda.sh
fi
# set anaconda path
export PATH=$PATH:/usr/local/anaconda/bin
conda update conda
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
# Let us save some space
conda clean --packages -y
# external tools
echo "Installing dependancies ... "
conda install -y bowtie2
conda install -y samtools
# Python (>2.7) with *pysam (>=0.8.3)*, *bx(>=0.5.0)*, *numpy(>=1.8.2)*, and *scipy(>=0.15.1)* libraries
conda install -y python=2.7.11
conda install -y -c anaconda scipy
conda install -y -c anaconda numpy
conda install -y -c bcbio bx-python
conda install -y -c bioconda pysam
# Install R
conda update readline
#conda install -c conda-forge readline=6.2
conda install -c r r-base
conda install -c r r-ggplot2=2.2.1
conda install -c r r-rcolorbrewer
conda install -c r r-gridbase
# Install HiC-pro
echo "Installing latest HiC-Pro release ..."
VERSION=$(curl -s https://github.com/nservant/HiC-Pro/releases/latest | egrep -o '2.[0-9]*.[0-9]*')
echo "v"$VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip
#VERSION="devel"
#echo $VERSION".zip" | wget --base=http://github.com/nservant/HiC-Pro/archive/ -i - -O hicpro_latest.zip && unzip hicpro_latest.zip
cd $(echo HiC-Pro-$VERSION)
# Edit the config-install.txt file to specify a SLURM cluster (this is the easiest solution short of forking the repo)
sed -i 's/CLUSTER_SYS.*/CLUSTER_SYS = SLURM/g' config-install.txt
make configure
make install
# Let us save some space
conda clean --packages -y
conda clean --all -y
rm -rf /usr/local/anaconda/pkgs
%test
INSTALLED_HICPRO_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname)
$INSTALLED_HICPRO_VERSION/HiC-Pro -h
%environment
export PATH=$PATH:/usr/local/anaconda/bin
INSTALLED_VERSION=$(find /usr/local/bin -name HiC-Pro | xargs dirname)
export PATH=$PATH:$INSTALLED_VERSION
export LANG=C
Collection
- Name: jdwheaton/singularity-ngs
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/jdwheaton-singularity-ngs-hicpro |
collection name | jdwheaton/singularity-ngs |
branch | master |
tag | hicpro |
commit | 3857750b13c01c1074d5f5a389879a5d996daed0 |
version (container hash) | e596ba1f2144f73477f0baeb6a05c60b |
build date | 2019-04-02T03:27:08.789Z |
size (MB) | 2097 |
size (bytes) | 650784799 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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