genetic engineering][ blat 자동 설치 및 자동 테스트 하기

genetic engineering][ blat 자동 설치 및 자동 테스트 하기

	#
	# swap 늘리기
	#
	swapoff -a
	sudo fallocate -l 10G /swapfile
	sudo mkswap /swapfile
	sudo swapon /swapfile
	swapon -a
	sudo swapon --show

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	sudo apt-get install libpng-dev
	sudo apt-get install zlib1g-dev
	sudo apt-get install libmysqlclient-dev
	sudo apt-get install libssl-dev openssl
	sudo apt-get install libcrypto++-dev
	sudo apt-get install curl
	pwd
	mkdir /tmp/blat && cd /tmp/blat
	wget http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc.zip
	unzip blatSrc.zip
	mkdir /home/hacker/bin/
	mkdir /home/hacker/bin/x86_64/
	cd /tmp/blat/blatSrc && make
	sudo cp ~/bin/x86_64/blat /usr/local/bin/blat
	blat
	for chr in `seq 1 22` X Y; do echo $chr; wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/chr$chr.fa.gz | gunzip -c - >> hg38.fa; done
	blat hg38.fa /dev/null /dev/null -makeOoc=hg39.fa.11.ooc -repMatch=1024
	curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_012920.1&rettype=fasta&retmode=text" >mtDNA.fa
	blat hg38.fa mtDNA.fa -ooc=hg39.fa.11.ooc sear.ps1

view raw blat.sh hosted with ❤ by GitHub

	wget https://gist.githubusercontent.com/ox1111/c8bb623a48565c6dcc3c89260b81f83f/raw/60fa6ad7293815489ac347f19382e362420c7534/blat.sh
	chmod 755 blat.sh
	./blat

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