Jaeyoung Chun hisplan

How to Add rsync to Git Bash for Windows 10

Download the package: http://www2.futureware.at/~nickoe/msys2-mirror/msys/x86_64/rsync-3.1.2-2-x86_64.pkg.tar.xz

Extract it and move rsync.exe to %HOMEDRIVE%%HOMEPATH%\AppData\Local\Programs\Git\usr\bin.

Flags:
	0x1	PAIRED        .. paired-end (or multiple-segment) sequencing technology
	0x2	PROPER_PAIR   .. each segment properly aligned according to the aligner
	0x4	UNMAP         .. segment unmapped
	0x8	MUNMAP        .. next segment in the template unmapped
	0x10	REVERSE       .. SEQ is reverse complemented
	0x20	MREVERSE      .. SEQ of the next segment in the template is reversed
	0x40	READ1         .. the first segment in the template
	0x80	READ2 .. the last segment in the template

from IPython.core.display import display, HTML
display(HTML("<style>.container { width:95% !important; }</style>"))

For CentOS

sudo yum group install "Development Tools"
sudo yum install ncurses-devel bzip2-devel xz-devel

cd /tmp
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar xvjf samtools-1.9.tar.bz2
cd samtools-1.9

conda install -c bioconda samtools=1.9=h8ee4bcc_1 openssl=1.0

sudo yum install git autoconf automake make gcc zlib-devel bzip2-devel xz-devel curl-devel openssl-devel
git clone https://github.com/samtools/htslib.git
cd htslib/
autoconf
autoheader
./configure
make
make test
sudo make install

conda create -n pysam python=3.6.5 pip

sudo yum install -y openssl-devel

wget https://github.com/pysam-developers/pysam/archive/v0.15.3.tar.gz
tar xvzf v0.15.3.tar.gz

cd pysam-0.15.3

Setting up Jupyter Notebook on AWS

Launch an AWS EC2 instance.

Install Miniconda:

wget https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh
bash Miniconda3-py38_4.10.3-Linux-x86_64.sh

	#!/bin/bash -e

	# http://hisham.hm/htop/

	yum groupinstall "Development Tools"
	yum install ncurses ncurses-devel
	wget http://hisham.hm/htop/releases/2.0.2/htop-2.0.2.tar.gz
	tar xvfvz htop-2.0.2.tar.gz
	cd htop-2.0.2

	docker rm $(docker ps -q -f 'status=exited')
	docker rmi $(docker images -q -f "dangling=true")
	docker volume rm $(docker volume ls -qf dangling=true)