bmichanderson/singularity-containers:unicycler
$ singularity pull shub://bmichanderson/singularity-containers:unicycler
Singularity Recipe
# Author: B. Anderson
# Singularity recipe for creating a container for using the program Unicycler
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER bmichanderson
PROGRAM Unicycler
VERSION latest
%post
# install essentials for obtaining and building software
apt update
apt upgrade -y
apt install -y autoconf automake build-essential cmake git libtool libpthread-stubs0-dev \
make python3-dev python3-setuptools wget zlib1g zlib1g-dev
# install additional dependencies
apt install -y bowtie2 ncbi-blast+ openjdk-11-jre samtools
# SPAdes
VERSION=3.13.0
URL=https://github.com/ablab/spades/releases/download/v"$VERSION"/SPAdes-"$VERSION"-Linux.tar.gz
wget "$URL"
tar -xzf SPAdes-"$VERSION"-Linux.tar.gz
rm SPAdes-"$VERSION"-Linux.tar.gz
echo "export PATH=$PATH:/SPAdes-$VERSION-Linux/bin" >> $SINGULARITY_ENVIRONMENT
# Pilon
VERSION=1.23
URL=https://github.com/broadinstitute/pilon/releases/download/v"$VERSION"/pilon-"$VERSION".jar
wget "$URL"
mv pilon-"$VERSION".jar /usr/local/bin/
# Racon
git clone --recursive https://github.com/isovic/racon.git racon
cd racon
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
make install
cd ../..
rm -r racon/
# Unicycler
git clone https://github.com/rrwick/Unicycler.git
cd Unicycler
./setup.py install
cd ../
rm -r Unicycler/
# test that the program works
unicycler --version
%help
******************************************************************************
This message is displayed when called as >singularity run-help unicycler.img
This container is meant to be used for running Unicycler
Execute it as >singularity exec unicycler.img unicycler [args]
Check contents by entering it as >singularity shell unicycler.img
******************************************************************************
Collection
- Name: bmichanderson/singularity-containers
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/bmichanderson-singularity-containers-unicycler |
collection name | bmichanderson/singularity-containers |
branch | master |
tag | unicycler |
commit | 1e140b633ee1c9db83765b86d47d0bb20338a05a |
version (container hash) | 1639700170405445749e904ff044d95a |
build date | 2021-03-24T21:42:20.929Z |
size (MB) | 1095 |
size (bytes) | 406212639 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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