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Jaeyoung Chun hisplan

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  • Memorial Sloan Kettering Cancer Center
  • New York, NY
  • 19:43 (UTC -04:00)
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@hisplan
hisplan / jupyter-notebook-wide-cell.md
Created March 15, 2019 21:25
jupyter notebook wide cell 
from IPython.core.display import display, HTML
display(HTML("<style>.container { width:95% !important; }</style>"))
@hisplan
hisplan / resolving-conda-install-samtools.md
Created July 24, 2019 15:27
Resolving conda install samtools 
conda install -c bioconda samtools=1.9=h8ee4bcc_1 openssl=1.0
@hisplan
hisplan / hgnc-rest-service-via-wget.md
Last active June 10, 2020 10:35
HGNC REST Service

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-rest-service-via-curl.md
Created June 10, 2020 10:34
Ensembl REST Service
@hisplan
hisplan / install-htop.sh
Last active February 20, 2020 14:33
Install htop
#!/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
hisplan / install-tree.sh
Created February 20, 2020 14:32
Install tree on Linux
#!/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
hisplan / cleanup.sh
Created January 25, 2020 21:58
Resolve Docker no space left issue
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
hisplan / install-pysam.md
Created July 29, 2019 19:38
Installing pysam on AWS Instance 
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
hisplan / how-to-install-bgzip-via-htslib.md
Last active July 26, 2019 14:36
bgzip via htslib 
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 / samtools.md
Created January 29, 2019 16:54
samtools 
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