Skip to content

Commit

Permalink
update instructions for latest course docker image
Browse files Browse the repository at this point in the history
  • Loading branch information
obigriffith committed Nov 18, 2024
1 parent e5c4d6f commit f2decc1
Show file tree
Hide file tree
Showing 2 changed files with 5 additions and 5 deletions.
4 changes: 2 additions & 2 deletions _posts/0000-07-01-Log_into_Compute.md
Original file line number Diff line number Diff line change
Expand Up @@ -161,15 +161,15 @@ First you will need to install docker. Typically this involves installing [Docke

1. Pull the image rnabio to your local Docker client with the tag 0.0.2 from the griffithlab repository:
```bash
docker pull griffithlab/rnabio:0.0.2
docker pull griffithlab/rnabio:0.0.3
```
2. Setup a local workspace directory for the RNAseq course. If you change the path or command used here in Step 2, make sure to update the path to the workspace directory accordingly in Step 3.
```bash
mkdir -p ~/rnabio-workspace
```
3. Initialize a Docker container using the image we pulled above. -v tells Docker to mount our workspace directory within the Docker container as /workspace with read-write priveleges. You'll see in the RNAseq course /workspace is the base directory for nearly all commands and steps. Note: we are running this docker container interactively and entering it at a bash shell prompt. We also switch the default user to "ubuntu" to match the RNAseq course tutorials.
```bash
docker run -v ~/rnabio-workspace:/workspace:rw --user ubuntu:ubuntu -it griffithlab/rnabio:0.0.2 /bin/bash
docker run -v ~/rnabio-workspace:/workspace:rw --user ubuntu:ubuntu -it griffithlab/rnabio:0.0.3 /bin/bash
```

The docker session should now be ready for the Unix tutorial and practical exercises.
6 changes: 3 additions & 3 deletions docker/course/ami_conversion_approach/README.txt
Original file line number Diff line number Diff line change
Expand Up @@ -50,15 +50,15 @@ nvme1n1
sudo mount /dev/nvme1n1p1 /mnt/

#13. Create a docker image from AMI root partition
sudo tar zcpP -C /mnt/ . | docker import - griffithlab/rnabio:0.0.2
sudo tar zcpP -C /mnt/ . | docker import - griffithlab/rnabio:0.0.3

#14. Test the image
mkdir -p ~/rnabio-workspace
docker run -v ~/rnabio-workspace:/workspace:rw --user ubuntu:ubuntu -it griffithlab/rnabio:0.0.2 /bin/bash
docker run -v ~/rnabio-workspace:/workspace:rw --user ubuntu:ubuntu -it griffithlab/rnabio:0.0.3 /bin/bash

#15. Login to dockerhub (you will need an account with permissions to push to the repo)
docker login

#16. Push the image to dockerhub
docker push griffithlab/rnabio:0.0.2
docker push griffithlab/rnabio:0.0.3

0 comments on commit f2decc1

Please sign in to comment.