Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update README.md to account for new Docker tagging system #675

Merged
merged 6 commits into from
Aug 26, 2022
Merged

Update README.md to account for new Docker tagging system #675

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
9efe8c4
Update README.md to account for new Docker tagging system
alex-l-kong Aug 25, 2022
0ea9a34
Merge branch 'main' into docker_tag_sec
alex-l-kong Aug 25, 2022
d788cf9
Merge branch 'main' into docker_tag_sec
alex-l-kong Aug 26, 2022
26a33e9
Nuke reference to having to build Docker locally
alex-l-kong Aug 26, 2022
991b1c8
Merge remote-tracking branch 'origin/docker_tag_sec' into docker_tag_sec
alex-l-kong Aug 26, 2022
7f3c771
Capitalization OCD
alex-l-kong Aug 26, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 6 additions & 18 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ Full documentation for the project can be found [here](https://ark-analysis.read
- [4. Spatial analysis](#4-spatial-analysis)
- [Installation Steps](#installation-steps)
- [Download the Repo](#download-the-repo)
- [Getting the Docker Image](#getting-the-docker-image)
- [Setting up Docker](#setting-up-docker)
- [Running on Windows](#running-on-windows)
- [Using the Repository (Running the Docker)](#using-the-repository-running-the-docker)
- [External Tools](#external-tools)
Expand Down Expand Up @@ -57,19 +57,11 @@ Then input the command:
git clone https://github.com/angelolab/ark-analysis.git
```

#### Getting the Docker Image
#### Setting up Docker

Next, you'll need to set up the Docker image with all of the required dependencies:
Next, you'll need to download Docker Desktop:
- First, [download](https://hub.docker.com/?overlay=onboarding) Docker Desktop.
- Once it's sucessfully installed, make sure it is running by looking in toolbar for the Docker whale icon.
- Once it's running, enter the following commands into terminal

```
cd ark-analysis
docker pull angelolab/ark-analysis:latest
```

You can now start to analyze your multiplexed imaging data!


#### Running on Windows
Expand All @@ -84,7 +76,9 @@ Enter the following command into terminal from the same directory you ran the ab
./start_docker.sh
```

This will generate a link to a jupyter notebook. Copy the last URL (the one with `127.0.0.1:8888` at the beginning) into your web browser.
If running for the first time, or if our Docker image has updated, it may take a while to build and setup before completion.

This will generate a link to a Jupyter notebook. Copy the last URL (the one with `127.0.0.1:8888` at the beginning) into your web browser.

Be sure to keep this terminal open. **Do not exit the terminal or enter `control-c` until you are finished with the notebooks**.

Expand Down Expand Up @@ -198,12 +192,6 @@ First, get the latest version of the repository.
git pull
```

Check for Docker updates by running:

```
docker pull angelolab/ark-analysis:latest
```

Then, run the command below to update the Jupyter notebooks to the latest version
```
./start_docker.sh --update
Expand Down