PLINK
PLINK is a whole genome association analysis toolset.
This site introduces several ways to analyze genomic data and related things using Plink and Python.
- Developer Christopher Chang's interview : http://gigasciencejournal.com/blog/gwas-reloaded-extended-qa-plink1-9-author-chris-chang/
What Feynman hated worse than anything else was intellectual pretense: phoniness, false sophistication, jargon.
by Leonard Susskind, an old friend of Feynman.
Wonyoung Cho.
Installation
sudo apt install plink1.9
or
- Download page : https://www.cog-genomics.org/plink2
$ wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20191028.zip
- if the plink is not a type of execute, then
$ sudo chmod u+x plink
- If it has something about permission, then
$ sudo chown user:user plink
- Download plink using Conda : https://anaconda.org/search?q=plink
$ conda install -c bioconda plink
Miniconda
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh
$ vi ~/.bashrc
export PATH="/home/username/miniconda3/bin:$PATH"
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda update conda
$ conda search --full-name python
$ conda create --name environment_name python=3.6.1
$ conda info --envs
$ source activate environment_name
$ source deactivate
Remove
$ conda remove --name environment_name --all
$ rm -rf ~/miniconda3
Document
- plink 1.07 document http://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf