connor-lab/snapper3:latest
$ singularity pull shub://connor-lab/snapper3:latest
Singularity Recipe
Bootstrap: docker
From: postgres:11
%post
apt-get -y update && apt-get -y upgrade
apt-get -y install curl git make
apt-get -y install bzip2 libbz2-dev g++ libncurses5-dev openjdk-8-jdk-headless unzip liblzma-dev zlib1g-dev
apt-get -y install python-dev python-pip
pip install cython
pip install argparse bintrees biopython psycopg2-binary paramiko PyVCF PyYAML hashids joblib
pip install git+https://github.com/m-bull/PHEnix.git
cd /opt
git clone https://github.com/connor-lab/snapper3.git
# SAMtools
curl -fsSL 'https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2' | tar -xj -C /tmp/
cd /tmp/samtools-1.9 && ./configure && make && make install
rm -rf /tmp/samtools-1.9
# BCFtools
curl -fsSL 'https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2' | tar -xj -C /tmp/
cd /tmp/bcftools-1.9 && ./configure && make && make install
rm -rf /tmp/bcftools-1.9
# Minimap2
cd /tmp
git clone https://github.com/lh3/minimap2 /tmp/minimap2
cd /tmp/minimap2
make
mv /tmp/minimap2/minimap2 /usr/local/bin/
rm -rf /tmp/minimap2
# BWA
cd /tmp
git clone https://github.com/lh3/bwa /tmp/bwa
cd /tmp/bwa
make
mv /tmp/bwa/bwa /usr/local/bin/
rm -rf /tmp/bwa
# Picard
curl -fsSL 'https://github.com/broadinstitute/picard/releases/download/2.18.16/picard.jar' --output /usr/local/bin/picard.jar
# GATK
curl -fsSL 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef' | tar -xj -C /usr/local/bin
find /usr/local/bin/GenomeAnalysisTK* -name "GenomeAnalysisTK.jar" -exec ln -s {} /usr/local/bin \;
# FastTree
curl -fsSL 'http://www.microbesonline.org/fasttree/FastTreeDbl' --output /usr/local/bin/FastTree
chmod +x /usr/local/bin/FastTree
%environment
export PICARD_JAR=/usr/local/bin/picard.jar
export GATK_JAR=/usr/local/bin/GenomeAnalysisTK.jar
export PATH=/opt/snapper3/scripts:$PATH
export PYTHONPATH=/opt/snapper3:/opt/snapper3/scripts:$PYTHONPATH
%labels
Maintainer m-bull
Version snapperdb-m-bull-git-latest
Collection
- Name: connor-lab/snapper3
- License: GNU General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-snapper3-latest |
collection name | connor-lab/snapper3 |
branch | master |
tag | latest |
commit | 6ddc483dc69ae59dbee49ee960c8691b02556493 |
version (container hash) | 05864b0f5b9701dbb3bbf72e8497aeaa |
build date | 2019-07-29T21:48:55.229Z |
size (MB) | 1147.0 |
size (bytes) | 475938847 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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