nealplatt/sH_hybridization:latest
$ singularity pull shub://nealplatt/sH_hybridization:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:16.04
%labels
AUTHOR Roy "Neal" Platt
MAINTAINER rplatt@txbiomed.org
VERSION 0.1
DATE 5 Feb 2018
%post
apt-get update
apt-get clean
apt-get install -qy \
wget \
bzip2 \
r-base \
r-base-dev \
default-jre \
bwa \
samtools \
git \
zip \
nano \
vim \
dialog
mkdir /usr/software
cd /usr/software/
#Install bioconda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
bash ./Miniconda3-latest-Linux-x86_64.sh -b -p /usr/software/miniconda3
export PATH="/usr/software/miniconda3/bin:$PATH"
conda install -y -c bioconda snakemake
rm Miniconda3-latest-Linux-x86_64.sh
ln -s /usr/software/miniconda3/bin/* /usr/local/bin/
#Install GATK
wget https://github.com/broadinstitute/gatk/releases/download/4.0.1.1/gatk-4.0.1.1.zip
unzip gatk-4.0.1.1.zip
rm gatk-4.0.1.1.zip
ln -s /usr/software/gatk-4.0.1.1/gatk /usr/local/bin/
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
unzip Trimmomatic-0.36.zip
ln -s /usr/software/Trimmomatic-0.36/trimmomatic-0.36.jar /usr/software/
rm -r Trimmomatic-0.36.zip Trimmomatic-0.36
#%runscript
# exec /bin/bash
Collection
- Name: nealplatt/sH_hybridization
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/nealplatt-sH_hybridization-latest |
collection name | nealplatt/sH_hybridization |
branch | master |
tag | latest |
commit | 83fcebaa5cbc92da7581aaca36ead0358ed4f660 |
version (container hash) | a16cb090803aab238c9c11d5866f6147 |
build date | 2018-02-06T23:37:02.039Z |
size (MB) | 2595 |
size (bytes) | 1360052255 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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