mvdenbog/BwaSamtoolsSingle:latest
$ singularity pull shub://mvdenbog/BwaSamtoolsSingle:latest
Singularity Recipe
Bootstrap: docker
From: centos:7.4.1708
%help
This is a container for executing SnapAligner and 2 python3 scripts to plot the results.
%setup
# make sure the "/pipeline/scripts" folder exists
# mkdir -p ${SINGULARITY_ROOTFS}/pipeline/scripts
# make sure the "/data" folder exists
# mkdir ${SINGULARITY_ROOTFS}/data
mkdir ${SINGULARITY_ROOTFS}/pasteur
%post
# Enable repo
yum -y install epel-release
yum-config-manager --enable epel
# Enable repo for installing python36 where you can "easily" install tkinter (we need it for the plotting python scripts, after doing snap):
# Install gcc compiler and zlib (we need it to compile snap, htslib, samtools):
yum -y install gcc
yum -y install zlib zlib-devel
yum -y install wget bzip2 ncurses ncurses-devel
# Install Python (3.6.5), pip and Snakemake
yum -y install https://centos7.iuscommunity.org/ius-release.rpm
# install snap (we need g++ too):
yum -y install git make gcc-c++
yum -y install python python-pip python-devel
pip install --upgrade pip
pip install matplotlib
# install samtools 0.6.2
cd /opt/
wget -O samtools-0.1.19.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download
tar xjf samtools-0.1.19.tar.bz2
cd samtools-0.1.19
make
chown -R root:root /opt/samtools-0.1.19
chmod -R a+rx /opt/samtools-0.1.19
cd /opt/
wget http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2
tar xjf bwa-0.6.2.tar.bz2
cd bwa-0.6.2
make
chown -R root:root /opt/bwa-0.6.2
chmod -R a+rx /opt/bwa-0.6.2
echo 'export PATH=$PATH:/opt/samtools-0.1.19/:/opt/samtools-0.1.19/bcftools/:/opt/bwa-0.6.2/' >> $SINGULARITY_ENVIRONMENT
%files
# Copy pipeline scripts
bwa_samtools_se.sh /opt/
depth_of_coverage_v2.py /opt/
%runscript
sh /opt/bwa_samtools_se.sh "$@"
%labels
MAINTAINER Mathias Vandenbogaert
VERSION 01
%test
Collection
- Name: mvdenbog/BwaSamtoolsSingle
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mvdenbog-BwaSamtoolsSingle-latest |
collection name | mvdenbog/BwaSamtoolsSingle |
branch | master |
tag | latest |
commit | 0b8e7c414fd0b14453b9478e7e6382622db881ff |
version (container hash) | 749ac5cadab399f9e56681c315dfe6e5 |
build date | 2019-05-19T12:12:34.432Z |
size (MB) | 614 |
size (bytes) | 240091167 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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