Ensembl REST Service
ID Lookup
https://rest.ensembl.org/documentation/info/lookup
curl -H 'Content-type:application/json' -sS 'https://rest.ensembl.org/lookup/id/ENSG00000237989?' | jq
# check if Python is running in 32-bit or 64-bit | |
# | |
# python -c "import struct;print(struct.calcsize('P')*8)" | |
# | |
import struct | |
# will return 32 for 32-bit, 64 for 64-bit | |
print(struct.calcsize("P") * 8) |
https://rest.ensembl.org/documentation/info/lookup
curl -H 'Content-type:application/json' -sS 'https://rest.ensembl.org/lookup/id/ENSG00000237989?' | jq
HGNC: Hugo Gene Nomenclature Committee
https://www.genenames.org/help/rest/
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
.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
#!/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 |
#!/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) |
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
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
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