diff --git a/README.md b/README.md index 37cd4dd009c8ea003c4c7020f8919fb05ed5a48a..8f193ff9731b06282e3ccc78d00ead538edbbca4 100644 --- a/README.md +++ b/README.md @@ -61,6 +61,29 @@ The ouput file is an unsorted list of files in uncompressed ASCII. Further proc ## Processing the output file +### Gitlab Container Registry Authentication + +Some automated tools in this repository use a container for processing to simplify environment management. The container itself is built using the spec in ./Dockerfile and available at `gitlab.rc.uab.edu:4567/<group>/gpfs-policy`. The shell scripts will automatically download this container if it is not detected in the working directory. + +In order to access the container, you will need to add a personal access token from your Gitlab account and register it to Singularity since the repository is not public. Do the following: + +1. Go to `gitlab.rc.uab.edu` and sign in with your BlazerID and password +2. Click your user icon in the top left and select `Preferences` +3. Select `Access Tokens` in the left menu +4. Click `Add New Token` + 1. Give the token a name (i.e. `Cheaha Singularity`) + 2. Remove the expiration date. It will default to one year from registration + 3. Add the `read_registry` scope + 4. Select `Create personal access token` +5. In the green box, click the button to copy the token +6. On Cheaha, create a text file in a secure spot and paste the token there. +7. Run `cat <token_file> | singularity registry login -u $USER --password-stdin docker://gitlab.rc.uab.edu:4567` + 1. If it succeeds, you will see a message similar to `INFO: Token stored in $HOME/.singularity/docker-config.json` +8. Delete the text file with the access token +9. Test access by pulling the container. For example: + - `singularity pull gpfs.sif docker://gitlab.rc.uab.edu:4567/<owner>/gpfs-policy:latest` + - Replace `<owner>` with the owner of the repo you're pulling from. Containers built in forks of a repository will have their containers in the forked registry + ### Split and compress ### Pre-parse output for Python