hisplan

Ensembl REST Service

https://rest.ensembl.org/

ID Lookup

https://rest.ensembl.org/documentation/info/lookup

curl -H 'Content-type:application/json' -sS 'https://rest.ensembl.org/lookup/id/ENSG00000237989?' | jq

hisplan

HGNC REST Service

HGNC: Hugo Gene Nomenclature Committee

https://www.genenames.org/help/rest/

tl;dr;

• fetch: returns all the fields, does not accept wild cards or multiple queries)
• search: returns all possible entries with only the fields hgnc_id, symbol and score.

hisplan

Ensembl GTF file differences

FTP LIST

http://ftp.ensembl.org/pub/release-85/gtf/homo_sapiens/

../
CHECKSUMS                                          10-Jul-2016 22:16                 221
Homo_sapiens.GRCh38.85.abinitio.gtf.gz             09-Jul-2016 23:45             3366550

hisplan

#!/bin/bash -e

# http://mama.indstate.edu/users/ice/tree/

wget http://mama.indstate.edu/users/ice/tree/src/tree-1.8.0.tgz
tar xvzf tree-1.8.0.tgz
cd tree-1.8.0
make
make install prefix=$HOME

hisplan

#!/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

hisplan

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)

hisplan

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

hisplan

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

hisplan

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

hisplan

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