Fix indentation

SAFEHR-data · Dec 7, 2023 · 3c626a6 · 3c626a6
1 parent 6d443ac
commit 3c626a6
Showing 1 changed file with 73 additions and 68 deletions.
diff --git a/README.md b/README.md
@@ -30,81 +30,86 @@ HTTP API to process messages from the `pacs` queue and populate the raw orthanc
 <details>
 <summary>Install shared miniforge installation if it doesn't exist</summary>
 
-    Follow the suggestion for installing a central [miniforge](https://github.com/conda-forge/miniforge)
-    installation to allow all users to be able to run modern python without having admin permissions.
-
-    ```shell
-    # Create directory with correct structure
-    mkdir /gae/miniforge3
-    chgrp -R docker /gae/miniforge3
-    chmod -R g+rwxs /gae/miniforge3  # inherit group when new directories or files are created
-    setfacl -R -m d:g::rwX /gae/miniforge3
-    # Install miniforge
-    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
-    bash Miniforge3-$(uname)-$(uname -m).sh -p /gae/miniforge3 
-    conda update -n base -c conda-forge conda
-    conda create -n pixl_dev python=3.10.*
-    ```
-
-    The directory should now have these permissions
-
-    ```
-    > ls -lah /gae/miniforge3/
-    total 88K
-    drwxrws---+  19 jstein01 docker 4.0K Nov 28 12:27 .
-    drwxrwx---.  18 root     docker 4.0K Dec  1 19:35 ..
-    drwxrws---+   2 jstein01 docker 8.0K Nov 28 12:27 bin
-    drwxrws---+   2 jstein01 docker   30 Nov 28 11:49 compiler_compat
-    drwxrws---+   2 jstein01 docker   32 Nov 28 11:49 condabin
-    drwxrws---+   2 jstein01 docker 8.0K Nov 28 12:27 conda-meta
-    -rw-rws---.   1 jstein01 docker   24 Nov 28 11:49 .condarc
-    ...
-    ```
+Follow the suggestion for installing a central [miniforge](https://github.com/conda-forge/miniforge)
+installation to allow all users to be able to run modern python without having admin permissions.
+
+```shell
+# Create directory with correct structure
+mkdir /gae/miniforge3
+chgrp -R docker /gae/miniforge3
+chmod -R g+rwxs /gae/miniforge3  # inherit group when new directories or files are created
+setfacl -R -m d:g::rwX /gae/miniforge3
+# Install miniforge
+wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+bash Miniforge3-$(uname)-$(uname -m).sh -p /gae/miniforge3
+conda update -n base -c conda-forge conda
+conda create -n pixl_dev python=3.10.*
+```
+
+The directory should now have these permissions
+
+```shell
+> ls -lah /gae/miniforge3/
+total 88K
+drwxrws---+  19 jstein01 docker 4.0K Nov 28 12:27 .
+drwxrwx---.  18 root     docker 4.0K Dec  1 19:35 ..
+drwxrws---+   2 jstein01 docker 8.0K Nov 28 12:27 bin
+drwxrws---+   2 jstein01 docker   30 Nov 28 11:49 compiler_compat
+drwxrws---+   2 jstein01 docker   32 Nov 28 11:49 condabin
+drwxrws---+   2 jstein01 docker 8.0K Nov 28 12:27 conda-meta
+-rw-rws---.   1 jstein01 docker   24 Nov 28 11:49 .condarc
+...
+```
+
 </details>
 <details>
 
 <summary>If you haven't just installed the miniforge yourself, update your configuration</summary>
-    Edit `~/.bash_profile` to add `/gae/miniforge3/bin` to the PATH. for example
-
-    ```
-    PATH=$PATH:$HOME/.local/bin:$HOME/bin:/gae/miniforge3/bin
-    ```
-
-    Run the updated profile (or reconnect to the GAE) so that conda is in your PATH
-
-    ```shell
-    source ~/.bash_profile
-    ```
-
-    Initialise conda
-
-    ```shell
-    conda init bash
-    ```
-
-    Run the updated profile (or reconnect to the GAE) so that conda is in your PATH
-
-    ```shell
-    source ~/.bash_profile
-    ```
-
-    Activate an existing pixl environment
-
-    ```shell
-    conda activate pixl_dev
-    ```
+
+Edit `~/.bash_profile` to add `/gae/miniforge3/bin` to the PATH. for example
+
+```shell
+PATH=$PATH:$HOME/.local/bin:$HOME/bin:/gae/miniforge3/bin
+```
+
+Run the updated profile (or reconnect to the GAE) so that conda is in your PATH
+
+```shell
+source ~/.bash_profile
+```
+
+Initialise conda
+
+```shell
+conda init bash
+```
+
+Run the updated profile (or reconnect to the GAE) so that conda is in your PATH
+
+```shell
+source ~/.bash_profile
+```
+
+Activate an existing pixl environment
+
+```shell
+conda activate pixl_dev
+```
+
 </details>
 <details>
 <summary>Create an instance for the GAE if it doesn't already exist</summary>
-    Select a place for the deployment. On UCLH infrastructure this will be in `/gae`, so `/gae/pixl_dev` for example.
-
-    ```shell
-    mkdir /gae/pixl_dev
-    chgrp -R docker /gae/pixl_dev
-    chmod -R g+rwxs /gae/pixl_dev  # inherit group when new directories or files are created
-    setfacl -R -m d:g::rwX /gae/pixl_dev
-    # now clone the repository or copy an existing deployment
-    ```
+
+Select a place for the deployment. On UCLH infrastructure this will be in `/gae`, so `/gae/pixl_dev` for example.
+
+```shell
+mkdir /gae/pixl_dev
+chgrp -R docker /gae/pixl_dev
+chmod -R g+rwxs /gae/pixl_dev  # inherit group when new directories or files are created
+setfacl -R -m d:g::rwX /gae/pixl_dev
+# now clone the repository or copy an existing deployment
+```
+
 </details>
 
 ### 1. Choose deployment environment