As of 2023, the main Bioconductor archive storage has been moved to an Open Storage Network s3-compatible bucket.
The instructions below can be used to copy an archived version from the remote location to your local machine. While these instructions are using the AWS CLI for its s3 client, this can be replaced with any s3 client. For those familiar with s3, the following bucket information might be all you need:
| Endpoint | https://mghp.osn.xsede.org |
| Bucket Path | bir190004-bucket01/archive.bioconductor.org/packages/3.xx |
We offer two ways of using the AWS CLI. If you have a Docker-enabled machine, we recommend you use the AWS Docker container rather than go through the installation. Otherwise, you may follow the installation instructions for the AWS CLI.
Below is a shell script showcasing how one can sync a singular version from the archive to the local storage. This variation requires you have Docker installed and running. If you do not, you may follow the installation instructions from Docker.
#!/bin/bash
ARCHIVE_VER=3.14
DEST_DIR=/tmp/my/location
mkdir -p $DEST_DIR
docker run --rm -v $DEST_DIR:/mnt/biocdest amazon/aws-cli:2.11.6 \
s3 sync --no-sign-request --delete \
--endpoint-url https://mghp.osn.xsede.org \
s3://bir190004-bucket01/archive.bioconductor.org/packages/$ARCHIVE_VER /mnt/biocdest/$ARCHIVE_VER
You can subsequently remove the AWS CLI container image by using docker rmi amazon/aws-cli:2.11.6
Similarly, using the local AWS CLI, the s3 sync command can be used to sync an archived version to your local machine. This variation requires you to have the AWS CLI installed. If you don't, you may follow the installation instructions from Amazon.
#!/bin/bash
ARCHIVE_VER=3.14
DEST_DIR=/tmp/my/location
mkdir -p $DEST_DIR
aws s3 sync --no-sign-request --delete \
--endpoint-url https://mghp.osn.xsede.org \
s3://bir190004-bucket01/archive.bioconductor.org/packages/$ARCHIVE_VER $DEST_DIR/$ARCHIVE_VER
If you wish to uninstall the AWS CLI, see see the following instructions.