dominik-handler/AP_singu:hic-pro
$ singularity pull shub://dominik-handler/AP_singu:hic-pro
Singularity Recipe
Bootstrap: docker
From: conda/miniconda2
%labels
AUTHOR Nicolas Servant
%pre
%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
#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
#conda install -y python=2.7
# 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 -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)
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:$INSTALLED_VERSION
export LANG=C
%runscript
HiC-Pro "$@"
Collection
- Name: dominik-handler/AP_singu
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dominik-handler-AP_singu-hic-pro |
collection name | dominik-handler/AP_singu |
branch | master |
tag | hic-pro |
commit | a6c0056d8e8c4d4c71873356dd530b94bebf5f5a |
version (container hash) | 65b1eb652902ccd2b1d5f0900f30bb5f |
build date | 2019-07-03T15:00:58.377Z |
size (MB) | 2559 |
size (bytes) | 851484703 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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