hybpiper-yang-and-smith-rbgv-singularity.def

BootStrap: library 
From: ubuntu:20.04


%files


%post
	apt-get -y update
	apt-get install -y software-properties-common
	add-apt-repository universe
	apt-get -y update 
	apt-get -y install libwww-perl
	apt-get -y install curl
	apt-get -y install wget
	apt-get -y install git
	apt-get -y install time
	apt-get -y install locales
	apt-get -y install fonts-dejavu-core
	apt-get -y install build-essential
	apt-get -y install pkg-config
	apt-get -y install vim    
	apt-get -y install perl
	apt-get -y install cpanminus
	apt-get -y install unzip
	apt-get -y install libgl1 # neccesary for ete3, see https://github.com/etetoolkit/ete/issues/195

	locale-gen en_US.UTF-8
	echo "LANG=en_US.UTF-8" >> /etc/default/locale


	# Install Yang and Smith scripts:
	git clone https://github.com/chrisjackson-pellicle/Yang-and-Smith-RBGV-scripts.git

	# Need to have copy of trim_tips.py that does not start with an integer, as it is imported in to 11_prune_paralogs_MI.py
	cp Yang-and-Smith-RBGV-scripts/04_trim_tips.py Yang-and-Smith-RBGV-scripts/trim_tips.py


	# Install HmmCleaner:
	curl -OL https://www.cpan.org/authors/id/P/PH/PHRED/Archive-Zip-1.68.tar.gz
	tar -xvzf Archive-Zip-1.68.tar.gz
	cd Archive-Zip-1.68
	perl Makefile.PL
	make
	make test
	make install
	cd ..


	cpanm https://cpan.metacpan.org/authors/id/P/PE/PEVANS/Scalar-List-Utils-1.55.tar.gz
	cpanm https://cpan.metacpan.org/authors/id/E/ET/ETHER/Moose-2.2014.tar.gz
	cpanm Bio::MUST::Core
	cpanm Bio::MUST::Drivers


	# Install HMMER
	curl -OL http://eddylab.org/software/hmmer/hmmer-3.3.tar.gz
	tar -xvzf hmmer-3.3.tar.gz
	cd hmmer-3.3
	./configure
	make
	make install
	cd ..

	cpanm -f Bio::MUST::Apps::HmmCleaner


	# Install HybPiper and set up to run:
	git clone https://github.com/mossmatters/HybPiper.git
	git clone https://github.com/chrisjackson-pellicle/HybPiper-RBGV-scripts.git
	cp /HybPiper-RBGV-scripts/* /HybPiper

	if [ ! -d /usr/local/miniconda3 ]; then
		curl -OL https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh && \
		bash Miniconda3-py38_4.10.3-Linux-x86_64.sh -b -p /usr/local/miniconda3 && \
		rm Miniconda3-py38_4.10.3-Linux-x86_64.sh
	fi
	
	# set conda path:
	export PATH="/usr/local/miniconda3/bin:$PATH"

	# add bioconda channel:
	conda config --add channels defaults
	conda config --add channels bioconda
	conda config --add channels conda-forge

	# install programs using conda:
	conda install -y bioconda::iqtree=2.0.3
	conda install -y bioconda::mafft=7.471
	conda install -y bioconda::bbmap=38.86
	conda install -y conda-forge::biopython=1.74
	conda install -y bioconda::bowtie2=2.4.1
	conda install -y bioconda::samtools=1.9
	conda install -y bioconda::exonerate=2.4.0
	conda install -y bioconda::blast=2.9.0
	conda install -y conda-forge::parallel=20190922
	conda install -y bioconda::spades=3.13.1
	conda install -y bioconda::bwa=0.7.17
	conda install -y conda-forge::r-base=3.5.1
	conda install -y conda-forge::r-gplots=3.0.1
	conda install -y conda-forge::r-heatmap.plus=1.3
	conda install -y conda-forge::r-ggplot2=3.1.1
	conda install -y conda-forge::r-reshape2=1.4.3	
	conda install -y bioconda::trimal=1.4.1
	conda install -y bioconda:clustalo=1.2.4
	conda install -y bioconda::trimmomatic=0.39
	conda install -y conda-forge::ete3=3.1.2
	conda install -y bioconda::muscle=3.8.1551

	# install astral;
	curl -OL https://github.com/smirarab/ASTRAL/raw/master/Astral.5.7.7.zip
	unzip Astral.5.7.7.zip
	chmod -R a+rX Astral

	# install alv (terminal alignment viewer):
	/usr/local/miniconda3/bin/pip install alv

	# install FastTreeMP:
	mkdir fast-tree-install
	cd fast-tree-install
	curl -OL http://www.microbesonline.org/fasttree/FastTreeMP
	chmod ugo=rx FastTreeMP
	cd ..


%environment  
	export PATH="/usr/local/miniconda3/bin:$PATH"
	export PATH="/HybPiper":$PATH
	export PATH="/fast-tree-install:$PATH"

%runscript 
	echo "This Singularity image is for use with the hybpiper-yang-and-smith-rbgv-pipeline.nf script"

%labels 
	Author Chris_J