Plink_install/Mayumi

PLINKのインストール

Plink 1.90

[https://www.cog-genomics.org/plink2]よりダウンロード。
[mayumi_ad@dandelion ~]$ wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20200219.zip -P /tmp
...
plink_linux_x86_6 100%[==========>] 8.50M 4.28MB/s in 2.0s

2020-04-01 13:49:17 (4.28 MB/s) - ‘/tmp/plink_linux_x86_64_20200219.zip’ saved [8916366/8916366]

[mayumi_ad@dandelion ~]$ sudo unzip /tmp/plink_linux_x86_64_20200219.zip -d /opt/plink/plink-1.90-Linux_64bit
Archive: /tmp/plink_linux_x86_64_20200219.zip
inflating: /opt/plink/plink-1.90-Linux_64bit/plink  
 inflating: /opt/plink/plink-1.90-Linux_64bit/LICENSE  
 inflating: /opt/plink/plink-1.90-Linux_64bit/toy.ped  
 inflating: /opt/plink/plink-1.90-Linux_64bit/toy.map  
 inflating: /opt/plink/plink-1.90-Linux_64bit/prettify  

[mayumi_ad@dandelion ~]$ sudo cp /opt/plink/plink-1.90-Linux_64bit/plink /usr/local/bin/
[mayumi_ad@dandelion ~]$ ls /usr/local/bin/
plink
[mayumi_ad@dandelion ~]$ plink
PLINK v1.90b6.16 64-bit (19 Feb 2020) www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3

plink <input flag(s)...> [command flag(s)...] [other flag(s)...]
 plink --help [flag name(s)...]

Commands include --make-bed, --recode, --flip-scan, --merge-list,
    • write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
    • hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
    • blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
    • rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
    • model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
    • make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
    • meta-analysis, --epistasis, --fast-epistasis, and --score.

"plink --help | more" describes all functions (warning: long).
できた!
Jupyter Notebookでも、「!plink」で始めれば plink のコマンドが走ることを確認できた。
-- Mayumi 2020-04-01


Plink 1.07(古かった…)

(base) [mayumi_ad@dandelion ~]$ wget http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip -P /tmp/
Resolving zzz.bwh.harvard.edu (zzz.bwh.harvard.edu)... 170.223.178.73
Connecting to zzz.bwh.harvard.edu (zzz.bwh.harvard.edu)|170.223.178.73|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3971138 (3.8M) [application/zip]
Saving to: ‘/tmp/plink-1.07-x86_64.zip’

plink-1.07-x86_64.z 100%[===================>] 3.79M 958KB/s in 5.6s

2020-04-01 11:50:17 (695 KB/s) - ‘/tmp/plink-1.07-x86_64.zip’ saved [3971138/3971138]

[mayumi_ad@dandelion ~]$ sudo mkdir /opt/plink
[sudo] password for mayumi_ad:
[mayumi_ad@dandelion ~]$ sudo unzip /tmp/plink-1.07-x86_64.zip -d /opt/plink/
Archive: /tmp/plink-1.07-x86_64.zip
 creating: /opt/plink/plink-1.07-x86_64/
 inflating: /opt/plink/plink-1.07-x86_64/plink  
 inflating: /opt/plink/plink-1.07-x86_64/COPYING.txt  
 inflating: /opt/plink/plink-1.07-x86_64/test.map  
 inflating: /opt/plink/plink-1.07-x86_64/test.ped  
 inflating: /opt/plink/plink-1.07-x86_64/gPLINK.jar  
 inflating: /opt/plink/plink-1.07-x86_64/README.txt 
[mayumi_ad@dandelion ~]$ sudo cp /opt/plink/plink-1.07-x86_64/plink /usr/local/bin/
※/usr/local/binにexeファイルを置いておけば、パスを通す必要がない模様。
一般ユーザで確認。
(base) [mayumi@dandelion ~]$ plink --noweb
@----------------------------------------------------------@
PLINK! v1.07 10/Aug/2009
----------------------------------------------------------    
(C) 2009 Shaun Purcell, GNU General Public License, v2    
----------------------------------------------------------    
For documentation, citation & bug-report instructions:    
http://pngu.mgh.harvard.edu/purcell/plink/    
@----------------------------------------------------------@

Skipping web check... [ --noweb ]
Writing this text to log file [ plink.log ]
Analysis started: Wed Apr 1 13:38:09 2020

Options in effect:
  --noweb

Before frequency and genotyping pruning, there are 0 SNPs
0 founders and 0 non-founders found
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 0 SNPs

ERROR: Stopping as there are no SNPs left for analysis
PLINKを使える状態になった。
-- Mayumi 2020-04-01

Plink :: Anaconda

Anacondaで仮想環境 plink を作成し、そこにPlinkをインストールする。

(base) [mayumi@dandelion ~]$ conda info -e
# conda environments:
#
qrcode /home/mayumi/.conda/envs/qrcode
base * /opt/anaconda3

(base) [mayumi@dandelion ~]$ conda create -n plink
...

(base) [mayumi@dandelion ~]$ conda activate plink
(plink) [mayumi@dandelion ~]$ conda install -y jupyter
...

(plink) [mayumi@dandelion ~]$ conda install -c bioconda plink
...

(plink) [mayumi@dandelion ~]$ conda install -c bioconda/label/cf201901 plink
...

(plink) [mayumi@dandelion ~]$ ipython kernel install --user --name plink
Installed kernelspec plink in /home/mayumi/.local/share/jupyter/kernels/plink
(plink) [mayumi@dandelion ~]$ which jupyter
~/.conda/envs/plink/bin/jupyter

(plink) [mayumi@dandelion ~]$ conda info -e
# conda environments:
#
plink * /home/mayumi/.conda/envs/plink
qrcode /home/mayumi/.conda/envs/qrcode
base /opt/anaconda3
-- Mayumi 2020-03-21
インストールはできたが、Jupyter Notebook でどう呼び出すのか分からずスタック。
-- Mayumi 2020-04-01




  • 最終更新:2020-04-01 14:25:34

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