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MCR doesn't host bioconductor images anymore #52

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MCR doesn't host bioconductor images anymore #52

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67 changes: 12 additions & 55 deletions README.md
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Expand Up @@ -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)
Expand Down Expand Up @@ -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

<a name="mcr"></a>
### 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:<tag>

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.

<p class="back_to_top">[ <a href="#top">Back to top</a> ]</p>

<a name="aci"></a>
### 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,
Expand Down Expand Up @@ -542,27 +499,27 @@ 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'

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

Expand Down Expand Up @@ -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 \
Expand All @@ -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

Expand Down