Unverified Commit e4c29f64 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

singularity: remove module as they are pulled from docker since 0.4.0

parent 4184614b
#/bin/bash
singularity exec /sps/lbmc/common/singularity/bcftools:1.7.img bcftools $@
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
mkdir -p /sps /pbs /scratch
BCFTOOLS_VERSION=1.7
PACKAGES=bcftools=${BCFTOOLS_VERSION}*
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
%environment
export BCFTOOLS_VERSION=1.7
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/bcftools:1.7.img src/singularity_modules/bcftools/1.7/bcftools.def && \
singularity sign bin/bcftools:1.7.img
#/bin/bash
singularity exec /sps/lbmc/common/singularity/bedtools:2.25.0.img bedtools $@
Bootstrap: docker
From: ubuntu:16.04
%labels
MAINTAINER Laurent Modolo
%post
mkdir -p /sps /pbs /scratch
BEDTOOLS_VERSION=2.25.0
PACKAGES=bedtools=${BEDTOOLS_VERSION}*
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
%environment
export BEDTOOLS_VERSION=2.25.0
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/bedtools:2.25.0.img src/singularity_modules/bedtools/2.25.0/bedtools.def && \
singularity sign bin/bedtools:2.25.0.img
#/bin/bash
singularity exec /sps/lbmc/common/singularity/bioawk:1.0.img bioawk $@
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
mkdir -p /sps /pbs /scratch
BIOAWK_VERSION=1.0
PACKAGES="git \
build-essential \
ca-certificates \
zlib1g-dev \
byacc"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
git clone https://github.com/lh3/bioawk.git && \
cd bioawk && \
git checkout tags/v${BIOAWK_VERSION} && \
make && \
cd .. && \
mv bioawk/bioawk /usr/bin/ && \
rm -Rf bioawk
%environment
export BIOAWK_VERSION=1.0
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/bioawk:1.0.img src/singularity_modules/bioawk/1.0/bioawk.def && \
singularity sign bin/bioawk:1.0.img
#/bin/bash
singularity exec /sps/lbmc/common/singularity/bowtie:1.2.2.img bowtie $@
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
mkdir -p /sps /pbs /scratch
BOWTIE_VERSION=1.2.2
SAMTOOLS_VERSION=1.7
PACKAGES="bowtie=${BOWTIE_VERSION}* \
samtools=${SAMTOOLS_VERSION}*"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
%environment
export BOWTIE_VERSION=1.2.2
export SAMTOOLS_VERSION=1.7
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/bowtie:1.2.2.img src/singularity_modules/bowtie/1.2.2/bowtie.def && \
singularity sign bin/bowtie:1.2.2.img
#/bin/bash
singularity exec /sps/lbmc/common/singularity/bowtie2:2.3.4.1.img bowtie2 $@
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
mkdir -p /sps /pbs /scratch
BOWTIE2_VERSION=2.3.4.1
SAMTOOLS_VERSION=1.7
PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
samtools=${SAMTOOLS_VERSION}* \
perl=5.26.1*"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
%environment
export BOWTIE2_VERSION=2.3.4.1
export SAMTOOLS_VERSION=1.7
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/bowtie2:2.3.4.1.img src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def && \
singularity sign bin/bowtie2:2.3.4.1.img
#/bin/sh
sudo singularity build --force bin/bwa:0.7.17.img src/singularity_modules/bwa/0.7.17/bwa.def && \
singularity sign bin/bwa:0.7.17.img
#/bin/bash
singularity exec /sps/lbmc/common/singularity/bwa:0.7.17.img bwa $@
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
mkdir -p /sps /pbs /scratch
BWA_VERSION=0.7.17
SAMBLASTER_VERSION=0.1.24
PACKAGES=curl="7.58.0* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
mv sambamba /usr/bin/ && \
rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
cd bwa-${BWA_VERSION}/ && \
make && \
cp bwa /usr/bin && \
cd .. && \
rm -R bwa-${BWA_VERSION}/
curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
cd samblaster-v.${SAMBLASTER_VERSION}/ && \
make && \
cp samblaster /usr/bin && \
cd .. && \
rm -R samblaster-v.${SAMBLASTER_VERSION}/
%environment
export BWA_VERSION=0.7.17
export SAMBLASTER_VERSION=0.1.24
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/canu:1.6.img src/singularity_modules/canu/1.6/canu.def && \
singularity sign bin/canu:1.6.img
#/bin/bash
singularity exec /sps/lbmc/common/singularity/canu:1.6.img canu $@
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