Singularity.hybphaser

# Author: B. Anderson
# Singularity recipe for creating a container for using HybPhaser
# see: https://github.com/LarsNauheimer/HybPhaser/


Bootstrap: docker
From: r-base:4.0.0


%labels
	MAINTAINER bmichanderson
	PROGRAM HybPhaser
	VERSION 2.0


%help
	This container is for running HybPhaser scripts from Lars Nauheimer
	Scripts are stored in /HybPhaser (in the PATH)
	You will need a config.txt file in the current directory

	To run Rscripts, use: 
		singularity run -H $(pwd) hybphaser.sif [script_name]
	To run the bash scripts, use: 
		singularity exec hybphaser.sif [script_name]

	The list of scripts:
	1_generate_consensus_sequences.sh
	1a_count_snps.R
	1b_assess_dataset.R
	1c_generate_sequence_lists.R
	2_extract_mapped_reads.sh
	2a_prepare_bbsplit_script.R
	2b_collate_bbsplit_results.R
	3a_prepare_phasing_script.R
	3b_collate_phasing_stats.R
	4_merge_sequence_lists.R
	HybPhaser_Main_script.R


%post
	export DEBIAN_FRONTEND=noninteractive

	# install dependencies
	apt update && apt install -y --no-install-recommends \
		autoconf \
		automake \
		build-essential \
		cmake \
		gawk \
		git \
		libbz2-dev \
		make \
		openjdk-8-jre \
		wget \
		zlib1g-dev

	## R packages
	R -e 'install.packages("remotes", repos = "https://cloud.r-project.org/")'
	R -e 'require(remotes); install_version("ape", version = "5.4", repos = "https://cloud.r-project.org/")'
	R -e 'require(remotes); install_version("seqinr", version = "4.2-8", repos = "https://cloud.r-project.org/")'
	R -e 'require(remotes); install_version("stringr", version = "1.4.0", repos = "https://cloud.r-project.org/")'

	## BBMap scripts
	URL=https://sourceforge.net/projects/bbmap/files/latest/download
	wget "$URL"
	tar -xzf download && rm download
	
	## bcftools
	BCF_VER=1.9
	URL=https://github.com/samtools/bcftools/releases/download/"$BCF_VER"/bcftools-"$BCF_VER".tar.bz2
	wget "$URL"
	tar -xjf bcftools-"$BCF_VER".tar.bz2 && rm bcftools-"$BCF_VER".tar.bz2
	cd bcftools-"$BCF_VER"
	./configure --prefix=/usr
	make
	make install
	cd .. && rm -r bcftools-"$BCF_VER"

	## BWA
	git clone https://github.com/lh3/bwa.git
	cd bwa
	make
	mv bwa /usr/bin/
	cd .. && rm -r bwa

	## samtools
	SAM_VER=1.9
	URL=https://github.com/samtools/samtools/releases/download/"$SAM_VER"/samtools-"$SAM_VER".tar.bz2
	wget "$URL"
	tar -xjf samtools-"$SAM_VER".tar.bz2 && rm samtools-"$SAM_VER".tar.bz2
	cd samtools-"$SAM_VER"
	./configure --prefix=/usr
	make
	make install
	cd .. && rm -r samtools-"$SAM_VER"

	# clean-up
	apt autoremove -y && apt clean all

	# install HybPhaser scripts
	#git clone https://github.com/LarsNauheimer/HybPhaser.git
	# note: for any changes, use my git  
	git clone -b develop_b https://github.com/bmichanderson/HybPhaser.git
	chmod 755 HybPhaser/*.sh


%environment
	# Set up environmental variables within the container
	export PATH="$PATH":/bbmap:/HybPhaser


%runscript
	# This will be executed when the container is run (singularity run [container])
	Rscript /HybPhaser/"$@"