-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
230c132
commit 00d4fbd
Showing
5 changed files
with
60 additions
and
5 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -217,5 +217,33 @@ | |
| "About", | ||
| "CODE OF CONDUCT" | ||
| ] | ||
| }, | ||
| { | ||
| "objectID": "how_to_install.html#deploying-bon-in-a-box-locally", | ||
| "href": "how_to_install.html#deploying-bon-in-a-box-locally", | ||
| "title": "How to Install", | ||
| "section": "Deploying BON in a Box locally", | ||
| "text": "Deploying BON in a Box locally\nBON in a Box can be installed and ran on a local computer. While personal computers have less computing power than servers, it is more convenient for pipeline development, or when working with small examples. Users adding scripts and creating pipelines on their local computer can directly run them through BON in a Box.\nPrerequisites:\n\nA GitHub account, and git installed on your computer\nAt least 6GB of free space (RAM requirements depend on the script that is being run)\nA linux shell\n\nThis can be Terminal on a Mac or Git Bash on a PC\n\n\n\nStep 1: Install Docker\n\nInstall Docker here\n\nNote: It is not necessary to make an account\nTo test whether docker is added to the path of your terminal, run docker run --rm hello-world\nFor Mac users: Make sure to check the chip of your machine and download the correct version.\n\nIf there is an error message when running docker run --rm hello-world, see https://stackoverflow.com/a/71923962/3519951\nIf you encounter error no matching manifest for linux/arm64/v8 in the manifest list entries, export DOCKER_DEFAULT_PLATFORM. See https://stackoverflow.com/a/76404045/3519951.\nIf you have a Silicon chip, check “Use Rosetta for x86_64/amd64 emulation on Apple Silicon”. See issue #175.\n\nFor linux users: Make sure to add your user to the docker group\n\n\n\n\nStep 2: Generate SSH Key\n\nFirst, make sure that you do not already have an SSH key registered to your computer by running ls -al ~/.ssh in your terminal.\n\nIf you already have a key it will be called one of the following:\n\nid_rsa.pub\nid__ecdsa.pub\nid_ed25519.pub\n\n\nIf you do not already have a key, generate one by running ssh-keygen ed25519 -C \"[email protected]\" replacing the email with the email address associated with your GitHub account.\n\nThis will prompt you to make a password. We recommend skipping this because it becomes a hassle. You can keep pressing enter to skip these steps.\n\nTo check if you successfully generated the SSH key, you can run ls -al ~/.ssh in the terminal. Your SSH key should be there now.\nNow, open the file with your SSH key by running cat ~/.ssh/<name of SSH key> e.g. cat ~/.ssh/id_ed25519.pub and copy your SSH key.\nNow, add your SSH key to your GitHub account by going to GitHub settings > SSH and GPG keys and “New SSH key”. You can name this whatever you want and paste your SSH key into the “Key” field.\n\n\n\nStep 3: Clone repository\n\nClone repository (Windows users: do not clone the repo in a folder under OneDrive.) This can be done in terminal using the following code: git clone [email protected]:GEO-BON/bon-in-a-box-pipelines.git or in GitHub desktop.\n\n\n\nStep 4: Set environment file\n\nProvide the environment variables: - Open the newly cloned repository on your computer\n\nFind the file called runner-sample.env\nDuplicate the file and rename the copy to runner.env.\nFill the properties depending on what you intend to run. Include any API keys that you need to access data (e.g. GBIF or IUCN)\nAdjust any server option as you see fit.\n\nUsing a linux terminal (terminal on Mac or Git Bash), navigate to the folder of the cloned repository.\nIn the linux terminal, type ./server-up.sh\n\nMake sure the server is started from a linux terminal that is in the same folder as the cloned repository so it can access the files.\nMake sure you have docker open and running on your computer.\nThe first execution will be long, in order to download the micro-services. The next ones will be shorter or immediate, depending on the changes.\nNetwork problems may cause the process to fail. First try running the command again. Intermediate states are saved so not everything will be redone even when there is a failure.\nWindows users may need to turn on virtualization and other tools for Docker Desktop to work and update wsl (“wsl –update”, see https://docs.docker.com/desktop/troubleshoot/topics/#virtualization. Access to the BIOS may be required to enable virtualization)\n\n\n\n\nStep 5: Connect to server\n\nType http://localhost/ to open BON in a Box\nRun ./server-down.sh in a terminal to stop the server when done\nOn Windows, to completely stop the processes, you might have to run wsl --shutdown\n\nWhen modifying scripts in the /scripts folder, servers do not need to be restarted: - When modifying an existing script, simply re-run the script from the UI and the new version will be executed. - When adding or renaming scripts, refresh the browser page.\nWhen modifying pipelines in the /pipelines folder, servers do not need to be restarted: - In the pipeline editor, click save, paste the file to your file in the pipeline folder and run it from the “pipeline run” page. - When adding or renaming pipelines, refresh the browser page.\n\n\nDeploying without pulling the new server\nIf the server has already been deployed at least once, and low bandwith does not allow to download the latest version (this can be a few gigabytes), the server can be started with option ./server-up.sh --offline. Use with caution, since this may create errors if elements of the repository depend on new server features." | ||
| }, | ||
| { | ||
| "objectID": "how_to_contribute.html#how-to-write-a-script-video-tutorial", | ||
| "href": "how_to_contribute.html#how-to-write-a-script-video-tutorial", | ||
| "title": "How to Contribute", | ||
| "section": "How to write a script video tutorial", | ||
| "text": "How to write a script video tutorial" | ||
| }, | ||
| { | ||
| "objectID": "how_to_contribute.html#how-to-create-a-pipeline-video-tutorial", | ||
| "href": "how_to_contribute.html#how-to-create-a-pipeline-video-tutorial", | ||
| "title": "How to Contribute", | ||
| "section": "How to create a pipeline video tutorial", | ||
| "text": "How to create a pipeline video tutorial\n\nAnalysis workflows can be adapted to BON in a Box pipelines using a few simple steps. Once BON in a Box is installed on your computer, Pipelines can be edited and run locally by creating files in your local BON-in-a-box folder that was cloned from the GItHub repository. Workflows can be in a variety of languages, including R, Julia, and Python, and not all steps of the pipeline need to be in the same language.\nAnalysis workflows can be converted to BON in a Box pipelines with a few steps:" | ||
| }, | ||
| { | ||
| "objectID": "how_to_install.html#video-tutorial", | ||
| "href": "how_to_install.html#video-tutorial", | ||
| "title": "How to Install", | ||
| "section": "Video tutorial", | ||
| "text": "Video tutorial" | ||
| } | ||
| ] | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters