Cytoverse Docker Imageĭocker images are also provided based on the Docker images available from Bioconductor, with the Cytoverse packages pre-installed. The CytoML package after you have obtained the Docker image using the above docker pull command. Here, you can also simply use the gatingset_to_flowjo method from While you can use this tool directly from the command line following the usage instructions This is not required for using any other parts of the Cytoverse, but if it is functionality you require, please followĭocker’s installation instructions and then follow these instructions to get the appropriateĭocker image from Amazon ECR Public Gallery: docker pull /x4k5d9i7/cytoverse/gs-to-wsp:latest Is provided in the form of a Docker image so it will work on any user operating system so long as Docker is installed. Sole exception of the functionality to convert Cytoverse GatingSet objects in to FlowJo workspaces. The entire Cytoverse collection of packages is open-source and available from the repositiories listed above, with the Or manually from GitHub: devtools::install_github("RGLab/flowStats") Or manually from Bioconductor: BiocManager::install("flowStats") Installing or updating additional RGLab packages can be done in a similar manner, either by utilizing the cytoverse installer package: cytoverse::cytoverse_update(pkgs = "flowStats") To install from the development branches from GitHub: remotes::install_github("RGLab/cytoverse")Ĭytoverse::cytoverse_update(repo = "github") To install from the stable Bioconductor releases: remotes::install_github("RGLab/cytoverse") This package can be used to later update cytoverse packages from either Bioconductor or GitHub. It will show you all of the packages that will be installed before proceeding. The easiest way to install the cytoverse packages is by using the cytoverse installer package. If you are building from source on Windows, you will need to install Rtools and will need to follow some additional instructions for installing RProtoBufLib. The most up-to-date development versions can also be built from sources available from Github. If you have not already done so, you will need to install BiocManager by running the following in R: if (!requireNamespace("BiocManager", quietly = TRUE)) Both the latest stable releases of all Cytoverse packages and more up-to-date development builds can be installed from Bioconductor.
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