connor-lab/singularity-recipes:snapperdb
$ singularity pull shub://connor-lab/singularity-recipes:snapperdb
Singularity Recipe
Bootstrap: docker
From: centos:latest
%post
yum install -y epel-release
yum -y update
yum install -y git make
yum install -y bzip2 bzip2-devel gcc-c++ ncurses-devel java-1.8.0-openjdk-headless unzip xz-devel zlib-devel
yum install -y python-devel python2-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
pip install git+https://github.com/m-bull/snapperdb.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 \;
%environment
export PICARD_JAR=/usr/local/bin/picard.jar
export GATK_JAR=/usr/local/bin/GenomeAnalysisTK.jar
%labels
Maintainer m-bull
Version snapperdb-m-bull-git-latest
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-snapperdb |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | snapperdb |
commit | 28db0e500498d5e9487b8ea1d3b6190f7c6afacb |
version (container hash) | 5c1a44be7e0e6a0d5d7b01d2f4b5406c |
build date | 2019-06-17T19:35:29.682Z |
size (MB) | 939 |
size (bytes) | 399999007 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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