bmichanderson/singularity-containers:igv
$ singularity pull shub://bmichanderson/singularity-containers:igv
Singularity Recipe
# Author: B. Anderson
# Singularity recipe for creating a container for using the program IGV
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER bmichanderson
PROGRAM IGV
VERSION 2.4.16
%post
# install java and needed packages
apt update
apt upgrade -y
export DEBIAN_FRONTEND=noninteractive
apt install -y glib-networking-common libcanberra-gtk-module locales openjdk-8-jre unzip wget
# set locale
locale-gen en_US.UTF-8
dpkg-reconfigure locales -f noninteractive
update-locale en_US.UTF-8
# download IGV
VERSION=2.4.16
URL=http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_"$VERSION".zip
wget "$URL"
unzip IGV_"$VERSION".zip
echo "export PATH=$PATH:/IGV_$VERSION" >> $SINGULARITY_ENVIRONMENT
%environment
# set locale
export LC_ALL=en_US.UTF-8
%help
******************************************************************************
This message is displayed when called as >singularity run-help igv.img
This container is meant to be used for running IGV
Execute it as >singularity exec igv.img igv.sh
Check contents by entering it as >singularity shell igv.img
******************************************************************************
Collection
- Name: bmichanderson/singularity-containers
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/bmichanderson-singularity-containers-igv |
collection name | bmichanderson/singularity-containers |
branch | master |
tag | igv |
commit | 5de5d238ee3408730dc5302df3b4e0c109a824cc |
version (container hash) | e2749464efee81fdb6398e1f1299ec0c |
build date | 2018-12-07T19:40:53.960Z |
size (MB) | 514 |
size (bytes) | 219459615 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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