jdwheaton/singularity-ngs:chip_atac_post
$ singularity pull shub://jdwheaton/singularity-ngs:chip_atac_post
Singularity Recipe
Bootstrap: docker
From: centos:7
# This container holds Picard tools, bedtools2, IGVTools, deeptools, MACS2, homer, and subread necessary for post-processing
# and visualization of ATAC-seq and ChIP-seq data.
%post
# Install required build tools
yum -y update
yum -y install wget gcc-c++ make zlib-devel unzip which zip epel-release
yum -y install curl-devel python-devel python-pip perl
# We need java for Picard
yum -y install java-1.8.0-openjdk-devel
# Install the Picard 2.18.9 jar in root
wget https://github.com/broadinstitute/picard/releases/download/2.18.9/picard.jar
# Download bedtools
wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz
tar -xvzf bedtools-2.27.1.tar.gz
cd bedtools2
make
# Install IGVtools
cd /
wget http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip
unzip igvtools_2.3.98.zip
# Install deeptools
pip install deeptools
# Install MACS2
pip install macs2
# Install subread
cd /
wget https://sourceforge.net/projects/subread/files/subread-1.6.2/subread-1.6.2-Linux-x86_64.tar.gz
tar -xvzf subread-1.6.2-Linux-x86_64.tar.gz
# Install homer
mkdir /homer
cd /homer
wget http://homer.ucsd.edu/homer/configureHomer.pl
perl configureHomer.pl -install
perl /homer/.//configureHomer.pl -install mm10
%environment
export PATH=$PATH:/bedtools2/bin
export PATH=$PATH:/IGVTools
export PATH=$PATH:/subread-1.6.2-Linux-x86_64/bin
export PATH=$PATH:/homer/bin
Collection
- Name: jdwheaton/singularity-ngs
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/jdwheaton-singularity-ngs-chip_atac_post |
collection name | jdwheaton/singularity-ngs |
branch | master |
tag | chip_atac_post |
commit | 5f09f35d6cebc74de81a36aa6856a9a286d3a3bc |
version (container hash) | 47a7b9fadad824f0ee00535f23a753db |
build date | 2020-02-11T22:43:57.670Z |
size (MB) | 6668 |
size (bytes) | 2114383903 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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