genomeAssembly.def

bootstrap: docker
From: ubuntu:20.04

%post
	apt -y update
	apt -y install bc zip unzip wget tzdata
	apt -y install build-essential git cmake zlib1g zlib1g-dev
	apt -y install curl
	
	cd /opt
	mkdir bin
	
	apt-get -qq -y update 
    	apt-get -qq install -y --no-install-recommends \
	python3 \
	python3-dev \
        python3-pip \
        python3-wheel
        

	pip install biopython
	pip install pandas

	git clone https://github.com/lh3/wgsim
	cd wgsim
	gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm
	cd ..
	
	git clone https://github.com/aquaskyline/SOAPdenovo2
	cd SOAPdenovo2/
	sed -i -e "s/-lm/-lm -no-pie/" Makefile
	make
	cd ..
	
	git clone https://github.com/sanger-pathogens/assembly-stats.git
	cd assembly-stats/
	mkdir build
	cd build
	cmake ..
	make
	make install
	cd ../..
	
	wget https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_linux_amd64.tar.gz
	tar -xzf seqkit_linux_amd64.tar.gz 
	chmod a+x seqkit
	mv seqkit /opt/bin/
	\rm seqkit_linux_amd64.tar.gz 
	

	wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz
	tar -xzf ncbi-blast-2.13.0+-x64-linux.tar.gz
	\rm ncbi-blast-2.13.0+-x64-linux.tar.gz
	mv ncbi-blast-2.13.0+/bin/* /opt/bin

	cd ..
	
%environment
    export LC_ALL=C
    export PATH=$PATH:/opt/wgsim:/opt/SOAPdenovo2:/opt/ncbi-blast-2.130+/nin:/opt/bin

%labels
    Maintainer vpbrendel
    Version v1.1.0