From 63dced070d745e9b918e9423085b942f15ba01a8 Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Sun, 4 Sep 2022 08:42:01 -0400 Subject: [PATCH] MCR doesn't host bioconductor images anymore - The launch happens using Azure container instances, but the images are launched from Dockerhub. - Making required changes in documentation - This needs to be updated on the website as well. --- README.md | 67 ++++++++++--------------------------------------------- 1 file changed, 12 insertions(+), 55 deletions(-) diff --git a/README.md b/README.md index a4e63af..2e2ca0b 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,6 @@ or [Microsoft Azure Container Instances](https://azure.microsoft.com/en-us/servi - [Modifying Image Container](#modify) - [Singularity](#singularity) - [Microsoft Azure Container Instances](#msft) - * [Using containers hosted on Microsoft Container Registry](#mcr) * [Use Azure Container Instances to run bioconductor images on-demand on Azure](#aci) - [How to contribute](#contribute) - [Deprecation Notice](#deprecation) @@ -460,54 +459,12 @@ containers and their usage https://www.rocker-project.org/use/singularity/. ## Microsoft Azure Container Instances If you are a Microsoft Azure user, you have an option to run your -containers using images hosted on [Microsoft Container Registry](https://github.com/microsoft/ContainerRegistry). - -> Microsoft Container Registry (MCR) is the primary Registry for all Microsoft Published docker images that offers a reliable and trustworthy delivery of container images with a syndicated catalog - - -### Using containers hosted on Microsoft Container Registry - -You can learn more about the `bioconductor_docker` image hosted on -Micosoft Container Registry -[here](https://hub.docker.com/_/microsoft-bioconductor/). - -Pull the `bioconductor_docker` image from Microsoft Container -Registry, specifying your `tag` of choice. Check -[here](https://hub.docker.com/_/microsoft-bioconductor-bioconductor-docker) -for the list of tags under "Full Tag Listing": - - docker pull mcr.microsoft.com/bioconductor/bioconductor_docker: - -To pull the latest image: - - docker pull mcr.microsoft.com/bioconductor/bioconductor_docker:latest - -**Example: Run RStudio interactively from your docker container** - -To run RStudio in a web browser session, run the following and access -it from `127.0.0.1:8787`. The default user name is "rstudio" and you -can specify your password as the example below (here, it is set to -'bioc'): - - docker run --name bioconductor_docker_rstudio \ - -v ~/host-site-library:/usr/local/lib/R/host-site-library \ - -e PASSWORD='bioc' \ - -p 8787:8787 \ - mcr.microsoft.com/bioconductor/bioconductor_docker:latest - -To run RStudio on your terminal: - - docker run --name bioconductor_docker_rstudio \ - -it \ - -v ~/host-site-library:/usr/local/lib/R/host-site-library \ - -e PASSWORD='bioc' \ - -p 8787:8787 \ - mcr.microsoft.com/bioconductor/bioconductor_docker:latest R +containers using images hosted on Dockerhub.

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-### Use Azure Container Instances to run bioconductor images on-demand on Azure +## Use Azure Container Instances to run bioconductor images on-demand on Azure [Azure Container Instances or ACI](https://azure.microsoft.com/en-us/services/container-instances/#features) provide a way to run Docker containers on-demand in a managed, @@ -542,19 +499,19 @@ Follow [this tutorial](https://docs.microsoft.com/en-us/azure/container-instances/container-instances-quickstart) to get familiar with Azure Container Instances. -To run the bioconductor image hosted on Microsoft Container Registry -or MCR, create a new resource group in your Azure subscription. Then +To run the bioconductor image hosted on Dockerhub, create a new +resource group in your Azure subscription. Then run the following command using Azure CLI. You can customize any or all of the inputs. This command is adapted to run on an Ubuntu machine: az container create \ --resource-group resourceGroupName \ - --name mcr-bioconductor \ - --image mcr.microsoft.com/bioconductor/bioconductor_docker \ + --name aci-bioconductor \ + --image bioconductor/bioconductor_docker \ --cpu 2 \ --memory 4 \ - --dns-name-label mcr-bioconductor \ + --dns-name-label aci-bioconductor \ --ports 8787 \ --environment-variables 'PASSWORD'='bioc' @@ -562,7 +519,7 @@ When completed, run this command to get the fully qualified domain name(FQDN): az container show \ --resource-group resourceGroupName \ - --name mcr-bioconductor \ + --name aci-bioconductor \ --query "{FQDN:ipAddress.fqdn,ProvisioningState:provisioningState}" \ --out table @@ -640,9 +597,9 @@ Here is an example command to mount an Azure file share to an ACI running biocon az container create \ --resource-group resourceGroupName \ - --name mcr-bioconductor-fs \ - --image mcr.microsoft.com/bioconductor/bioconductor_docker \ - --dns-name-label mcr-bioconductor-fs \ + --name aci-bioconductor-fs \ + --image bioconductor/bioconductor_docker \ + --dns-name-label aci-bioconductor-fs \ --cpu 2 \ --memory 4 \ --ports 8787 \ @@ -656,7 +613,7 @@ When completed, run this command to get the fully qualified domain name or FQDN: az container show \ --resource-group resourceGroupName \ - --name mcr-bioconductor-fs \ + --name aci-bioconductor-fs \ --query "{FQDN:ipAddress.fqdn,ProvisioningState:provisioningState}" \ --out table