diff --git a/instructor_notes/openscpca/01_openscpca-setup.md b/instructor_notes/openscpca/01_openscpca-setup.md index 0606054..71805e5 100644 --- a/instructor_notes/openscpca/01_openscpca-setup.md +++ b/instructor_notes/openscpca/01_openscpca-setup.md @@ -26,57 +26,40 @@ The goal for this activity is to set everyone up on LSfR, but we if internet con - Explain that we are using VSCodium since we plan to write a Python module, but we could launch an RStudio instance for R development as well. Similarly, if we anticipated needing more computational resources, we could select different instance options. -4. While the instance is being created (~10 minutes), lead participants through some _local setup_: - - - [Set up conda](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-conda/) (assuming it has already been installed): - ```bash - # set up channels - conda config --add channels defaults - conda config --add channels bioconda - conda config --add channels conda-forge - conda config --set channel_priority strict - - # install packages into base - conda install awscli conda-lock jq pre-commit - ``` - - - [Configure AWS CLI](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/configure-aws-cli/) (may wish to show this website during configuration for prompt responses) - ```bash - # launch configuration and fill in prompts - aws configure sso - - # after configuration, log in (this will launch a browser) - aws sso login --profile openscpca - ``` - - - If we have time and/or it's clear we need to work locally, they can also clone their `OpenScPCA-analysis` fork, and [set up pre-commit](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-precommit/) via the GitKraken terminal +4. While the instance is being created (~10 minutes), lead participants through some _local setup_. +As needed for time, we can skip some of the later steps. + - [Clone the repo with GitKraken](https://openscpca.readthedocs.io/en/latest/technical-setup/clone-the-repo/) your `OpenScPCA-analysis` fork, and add `AlexsLemonade/OpenScPCA-analysis` as the upstream remote + - Set up the [conda environment](https://openscpca.readthedocs.io/en/latest/software-platforms/aws/starting-development-on-lsfr/#create-and-activate-a-conda-environment): + ```bash + # configure channels + conda config --add channels defaults + conda config --add channels bioconda + conda config --add channels conda-forge + conda config --set channel_priority strict + + # create openscpca environment + cd ~/{your disk's name}/OpenScPCA-analysis # or, do this from GitKraken terminal without needing to cd + conda env create -f environment.yml + + # activate + conda activate openscpca + ``` + - [Set up pre-commit](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-precommit/) via the GitKraken terminal with `pre-commit install` + - [Configure AWS CLI](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/configure-aws-cli/) (may wish to show this website during configuration for prompt responses) + ```bash + # launch configuration and fill in prompts + aws configure sso + + # after configuration, log in (this will launch a browser) + aws sso login --profile openscpca + ``` 5. Back on LSfR, [create a volume](https://openscpca.readthedocs.io/en/latest/software-platforms/aws/working-with-volumes/) and attach it to the VSCodium instance. -6. Finally, we can [launch the VSCodium instance](https://lfr.console.aws.amazon.com/ls/research/webapp/home/virtual-computers) and set up: - - First, launch from the "Access operating system" dropdown - - Set up the [conda environment](https://openscpca.readthedocs.io/en/latest/software-platforms/aws/starting-development-on-lsfr/#create-and-activate-a-conda-environment): - !! REVIEWER TODO: We are recommending installing into an openscpca environment here but into base environment for local setup. Do we want to change any docs? - ```bash - # configure channels - conda config --add channels defaults - conda config --add channels bioconda - conda config --add channels conda-forge - conda config --set channel_priority strict - - # create openscpca environment - cd ~/{your disk's name}/OpenScPCA-analysis - conda env create -f environment.yml - - # activate - conda activate openscpca - ``` - - - Clone the repo with GitKraken: - - Sign into GitKraken with GitHub credentials, if not already signed in - - [Clone](https://openscpca.readthedocs.io/en/latest/technical-setup/clone-the-repo/) your `OpenScPCA-analysis` fork, and add `AlexsLemonade/OpenScPCA-analysis` as the upstream remote - - - [Set up pre-commit](https://openscpca.readthedocs.io/en/latest/technical-setup/environment-setup/setup-precommit/) via the GitKraken terminal +6. Finally, we can [launch the VSCodium instance](https://lfr.console.aws.amazon.com/ls/research/webapp/home/virtual-computers) and set up. First, launch from the "Access operating system" dropdown, and: + - Sign into GitKraken and clone the fork + - Setup conda + - Setup pre-commit 7. _While keeping the instance window open_, return to the LSfR page to launch the instance as `VSCodium`. - We'll now have two browser windows: One with Ubuntu and one with VS Code that can be used side-by-side