/docker-cellranger-atac

Dockerized Cell Ranger ATAC

Primary LanguageShellMIT LicenseMIT

docker-cellranger-atac

Dockerized Cell Ranger ATAC v2.1.0

Build Container Image

SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/) is required for smooth and uninteruppted build process (e.g. CI/CD). For setup, please refer to this page. All the instructions below is given under the assumption that you have already configured SCING in your environment.

SCING installation is required.

conda activate scing

./build.sh

Push to Docker Registry

conda activate scing

./push.sh

Usage

$ docker run -it --rm cellranger-atac:2.1.0 --help

cellranger-atac cellranger-atac-2.1.0
Process 10x Genomics Chromium Single Cell ATAC data

USAGE:
    cellranger-atac <SUBCOMMAND>

OPTIONS:
    -h, --help       Print help information
    -V, --version    Print version information

SUBCOMMANDS:
    count        Count reads from a single Single Cell ATAC library
    mkfastq      Run bcl2fastq on Single Cell ATAC sequencing data
    mkref        Create a cellranger-atac-compatible reference package
    aggr         Aggregate data from multiple `cellranger-atac count` runs
    reanalyze    Re-run secondary analysis (dimensionality reduction, clustering, etc) on a
                 completed `cellranger-atac count` or `cellranger-atac aggr` run
    testrun      Run a tiny cellranger-atac count pipeline to verify software integrity
    upload       Upload analysis logs to 10x Genomics support
    sitecheck    Collect linux system configuration information
    help         Print this message or the help of the given subcommand(s)