Phil9S/genbiotools:latest

$ singularity pull shub://Phil9S/genbiotools:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:18.04

%setup

%files

%environment
	export LC_ALL=C

%post
	#update all
	apt-get update

	#get required linux distro 
	apt-get install -y wget git autoconf automake make gcc perl libncurses5-dev unzip \
			zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev \
			default-jdk python3.6
	
	#Clone and build htslib
    	git clone https://github.com/samtools/htslib.git
    	cd htslib/
    	autoheader && autoconf && ./configure && make && make install
	cd 

	#Download and build samtools
	wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
	bzip2 -d samtools-1.10.tar.bz2 && tar -xf samtools-1.10.tar
	cd samtools-1.10/
	./configure && make && make install
	cd

	#Download and build BCFtools
	wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2
	bzip2 -d bcftools-1.10.2.tar.bz2 && tar -xf bcftools-1.10.2.tar
	cd bcftools-1.10.2
	./configure && make && make install
	cd

	#Download and build bwa/bwakit-minimal
	wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
	bzip2 -d bwa-0.7.17.tar.bz2
	tar -xf bwa-0.7.17.tar
	cd bwa-0.7.17
	make
	cp bwa /usr/bin/
	cp bwakit/* /usr/bin/
	cd
	
	#Download and install bwa-mem2
	wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre1/bwa-mem2-2.0pre1_x64-linux.tar.bz2
	bzip2 -d bwa-mem2-2.0pre1_x64-linux.tar.bz2
	tar -xf bwa-mem2-2.0pre1_x64-linux.tar
	cp bwa-mem2-2.0pre1_x64-linux/* /usr/bin/

	#Download and build minimap2
	git clone https://github.com/lh3/minimap2
	cd minimap2 && make
	cp minimap2 /usr/bin/
	cd

	#Download and install freebayes
	wget https://github.com/ekg/freebayes/releases/download/v1.3.1/freebayes-v1.3.1
	chmod +u+x freebayes-v1.3.1
	cp freebayes-v1.3.1 /usr/bin/freebayes

	#Download and setup VarScan and making wrapper script
	wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar
	printf '#!/bin/bash\n$(java -jar /usr/bin/VarScan.v2.4.2.jar $*)' > VarScan
	chmod +u+x VarScan
	mv VarScan /usr/bin/
	mv VarScan.v2.4.2.jar /usr/bin/

	#Download and install GATK package
	wget https://github.com/broadinstitute/gatk/releases/download/4.1.4.1/gatk-4.1.4.1.zip
	unzip gatk-4.1.4.1.zip
	mv gatk-4.1.4.1/gatk-package-4.1.4.1-local.jar /usr/bin/
	mv gatk-4.1.4.1/gatk /usr/bin/
	ln /usr/bin/python3.6 /usr/bin/python
	
	#Download and install picard
	wget https://github.com/broadinstitute/picard/releases/download/2.21.6/picard.jar
	printf '#!/bin/bash\n$(java -jar /usr/bin/picard.jar $*)' > picard
	chmod +u+x picard
	mv picard /usr/bin/
	mv picard.jar /usr/bin/
	
	#Make output directory
	mkdir /data/
	
	#Clean up
	rm -r *
	apt-get check
	apt-get autoclean

%runscript
	echo "There is no RUN script for this container - Please use EXEC to use containerised applications."
	echo "See singularity run-help for more information."

%labels
    Author P.SMITH (CRUK-CI)
    Version v0.1

%help
    	This is container contains installations of mutiple genomic tools which can be utilised using the EXEC command.
	Included tools are:
	
	HTSlib (and susequent utilities)
	bwa
	bwa-mem2
	minimap2
	samtools
	bcftools
	gatk
	Picard
	freebayes
	VarScan

	Tools can be used as expected by preappending singularity exec [THIS_CONTAINER] [application] [commandlineOptions]

Collection

• Name: Phil9S/genbiotools
• License: GNU General Public License v3.0

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.