reorder and move instructions to the first time they happen

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