spashleyfu/plink2_snakemake repository overview

➜  plink2_snakemake docker build -t plink2_tset .                   
[+] Building 73.7s (9/9) FINISHED                                                                                                           
 => [internal] load build definition from Dockerfile                                                                                   0.0s
 => => transferring dockerfile: 1.19kB                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                      0.0s
 => => transferring context: 2B                                                                                                        0.0s
 => [internal] load metadata for docker.io/library/debian:stretch-slim@sha256:d27bbe1259aeb6bed459440649ce5bda9083ab9782274c7bc469f02  0.0s
 => CACHED [1/5] FROM docker.io/library/debian:stretch-slim@sha256:d27bbe1259aeb6bed459440649ce5bda9083ab9782274c7bc469f02f283a9e18    0.0s
 => [2/5] RUN apt-get update --fix-missing &&   apt-get install -y wget bzip2 build-essential   less vim   ca-certificates git libgl  36.6s
 => [3/5] RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh &&   /bin/bash ~/  12.1s
 => [4/5] RUN conda install -n base -c conda-forge mamba                                                                              16.1s
 => [5/5] RUN mamba install -n base -c conda-forge -c bioconda   snakemake plink2                                                     59.0s
 => exporting to image                                                                                                                14.6s
 => => exporting layers                                                                                                               14.6s
 => => writing image sha256:2f4fbc364b7f4441bf9d5c0587709e28813925aed617b9a40f9d5fc507932218                                           0.0s 
 => => naming to docker.io/library/plink2_tset                                                                                         0.0s 


(base) root@15c94f00f40c:/# snakemake --version
6.4.1
(base) root@15c94f00f40c:/# plink2 
PLINK v2.00a2.3LM 64-bit Intel (24 Jan 2020)   www.cog-genomics.org/plink/2.0/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3

  plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]
  plink2 --help [flag name(s)...]

Commands include --rm-dup list, --make-bpgen, --export, --freq, --geno-counts,
--sample-counts, --missing, --hardy, --indep-pairwise, --ld, --sample-diff,
--make-king, --king-cutoff, --write-samples, --write-snplist, --make-grm-list,
--pca, --glm, --adjust-file, --score, --variant-score, --genotyping-rate,
--pgen-info, --validate, and --zst-decompress.

"plink2 --help | more" describes all functions.

➜  plink2_snakemake docker push spashleyfu/plink2_snakemake:latest
The push refers to repository [docker.io/spashleyfu/plink2_snakemake]
281ba79b8f20: Pushed 
dfc203ceb9b6: Pushed 
76ba51d433ea: Pushed 
084bbba1d989: Pushed 
e4b1e8d0745b: Mounted from spashleyfu/knight_bam_metrics 
latest: digest: sha256:d2df87acdbfdef2691ab259050a3fec10f5a671afeb7ab8fc470febefc7fd462 size: 1380