spashleyfu/bcftools_snakemake repository overview

➜  bcftools_snakemake docker build -t bcftools_test .                        
[+] Building 140.6s (10/10) 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:d27bbe1259aeb6bed459440649ce5bda9083ab9782274c7bc469f02f283a9e18           0.7s
 => [auth] library/debian:pull token for registry-1.docker.io                                                                                            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 libglib2.0-0 libxext6 l  36.6s
 => [3/5] RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh &&   /bin/bash ~/miniconda.sh -b -p  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 bcftools                                                                     55.9s 
 => exporting to image                                                                                                                                  19.1s 
 => => exporting layers                                                                                                                                 19.1s 
 => => writing image sha256:c69d3cba69c9f56cc4b29d4d30088fa8c17d0e84f4d1300e9b55e56a0564b025                                                             0.0s 
 => => naming to docker.io/library/bcftools_test                                                                                                         0.0s 
➜  bcftools_snakemake docker run --rm -it bcftools_test /bin/bash     
(base) root@9c914ca525c0:/# snakemake --version
6.4.1
(base) root@9c914ca525c0:/# bcftools 

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
License: GNU GPLv3+, due to use of the GNU Scientific Library
Version: 1.12 (using htslib 1.12)

Usage:   bcftools [--version|--version-only] [--help] <command> <argument>

Commands:

 -- Indexing
    index        index VCF/BCF files

 -- VCF/BCF manipulation
    annotate     annotate and edit VCF/BCF files
    concat       concatenate VCF/BCF files from the same set of samples
    convert      convert VCF/BCF files to different formats and back
    isec         intersections of VCF/BCF files
    merge        merge VCF/BCF files files from non-overlapping sample sets
    norm         left-align and normalize indels
    plugin       user-defined plugins
    query        transform VCF/BCF into user-defined formats
    reheader     modify VCF/BCF header, change sample names
    sort         sort VCF/BCF file
    view         VCF/BCF conversion, view, subset and filter VCF/BCF files

 -- VCF/BCF analysis
    call         SNP/indel calling
    consensus    create consensus sequence by applying VCF variants
    cnv          HMM CNV calling
    csq          call variation consequences
    filter       filter VCF/BCF files using fixed thresholds
    gtcheck      check sample concordance, detect sample swaps and contamination
    mpileup      multi-way pileup producing genotype likelihoods
    polysomy     detect number of chromosomal copies
    roh          identify runs of autozygosity (HMM)
    stats        produce VCF/BCF stats

 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
 automatically even when streaming from a pipe. Indexed VCF and BCF will work
 in all situations. Un-indexed VCF and BCF and streams will work in most but
 not all situations.

(base) root@2607eb58706a:/# conda --version
conda 4.10.1

➜  bcftools_snakemake docker push spashleyfu/bcftools_snakemake:latest
The push refers to repository [docker.io/spashleyfu/bcftools_snakemake]
0c522e913a67: Pushed 
dfc203ceb9b6: Pushed 
76ba51d433ea: Mounted from spashleyfu/plink2_snakemake 
084bbba1d989: Pushed 
e4b1e8d0745b: Mounted from spashleyfu/plink2_snakemake 
latest: digest: sha256:9bbedb465a1eb309012e1b0d6bc95d4cc9cce4fa8a85b7634c615dc8fee02795 size: 1380