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Focusing

Jaeyoung Chun hisplan

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Focusing
  • Memorial Sloan Kettering Cancer Center
  • New York, NY
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View ensembl-rest-service-via-curl.md
View hgnc-rest-service-via-wget.md

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
hisplan / ensembl-gtf-file-diffs.md
Last active May 26, 2021
Ensembl GTF file differences
View ensembl-gtf-file-diffs.md
@hisplan
hisplan / install-tree.sh
Created Feb 20, 2020
Install tree on Linux
View install-tree.sh
#!/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
View install-htop.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
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hisplan / cleanup.sh
Created Jan 25, 2020
Resolve Docker no space left issue
View cleanup.sh
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)
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hisplan / jupyter-notebook-on-aws.md
Last active Nov 13, 2021
Setting up Jupyter Notebook on AWS
View jupyter-notebook-on-aws.md

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
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hisplan / install-pysam.md
Created Jul 29, 2019
Installing pysam on AWS Instance
View install-pysam.md
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
View how-to-install-bgzip-via-htslib.md
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
hisplan / resolving-conda-install-samtools.md
Created Jul 24, 2019
Resolving conda install samtools
View resolving-conda-install-samtools.md
conda install -c bioconda samtools=1.9=h8ee4bcc_1 openssl=1.0