HugoMananet/OutLyzer:outlyzer.2.0.def

$ singularity pull shub://HugoMananet/OutLyzer:outlyzer.2.0.def

Singularity Recipe

#!/bin/bash
Bootstrap: docker
From: phusion/baseimage:0.10.2


%label

	MAINTAINER Hugo Mananet
	VERSION 2.0
	
	
%post

	mkdir /soft
	mkdir /work
	mkdir /user1
	mkdir /user2
	mkdir /tmp3

	apt-get -y update
	apt-get -y install build-essential \
	wget \
	make \
	gcc \
	autoconf \
	perl \
	ca-certificates \
	curl \
	libbz2-dev \
	liblzma-dev \
	libncurses5-dev \
	libncursesw5-dev \
	zlib1g-dev \
	python2.7 \
	python-setuptools \
	python-dev \
	python-wheel \
	python-subprocess32 \
	python-numpy \
	python-scipy \
	libpython2.7-stdlib \
	python-pip

	pip install --upgrade pip
	python2.7 -m pip install multiprocessing
	
	mkdir -p /opt/
	wget https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2 && mv samtools-1.3.tar.bz2 /opt/
	cd /opt/ && tar xjvf samtools-1.3.tar.bz2

	cd /opt/samtools-1.3/ && ./configure && make
	cd /opt/ && rm samtools-1.3.tar.bz2

	ln -s /opt/samtools-1.3/samtools /bin
	ln -s /opt/samtools-1.3/misc/* /bin
	
	wget -P /opt/ https://github.com/EtieM/outLyzer/archive/v2.tar.gz
	# mv v2.tar.gz /opt/v2.tar.gz
	cd /opt/ && tar xzvf v2.tar.gz
	rm /opt/v2.tar.gz 
	## ou "v2" uniquement (a tester)
	
	chmod 755 /opt/outLyzer-2/outLyzer.py
	ln -s /opt/outLyzer-2/outLyzer.py /usr/local/bin/outlyzer.py
	
	
%environment

	# export samtools=/path/to/samtools
	
%runscript

	exec outlyzer.py "$@"

Collection

• Name: HugoMananet/OutLyzer
• License: None

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.