Update CLI docs

docs/cli/docker.md

@@ -37,8 +37,8 @@ You can also reference a `<version>` in the run command. For example:
 
     docker run -it --rm neuroscout/neuroscout-cli:version-0.5.1 run Mv3ev /out
 
-!!! note
-`master` is a special tag name which refers to the most recent _unstable_ commit to GitHub. 
+!!! Note
+    `master` is a special tag name which refers to the most recent _unstable_ commit to GitHub. 
 
 ## Saving outputs to disk
 
@@ -52,9 +52,9 @@ Here we mount the local `/home/user/out` directory to `/out` on the container.:
 
     docker run -it --rm -v /home/user/out:/out neuroscout/neuroscout-cli run 5xH93 /out 
 
-!!! note
-After the `run` command, we are telling _neuroscout-cli_ to save the outputs to the `/out` directory on `Docker`,
-which is mapped to `/home/user/out` on our local system.
+!!! Note
+    After the `run` command, we are telling _neuroscout-cli_ to save the outputs to the `/out` directory on `Docker`,
+    which is mapped to `/home/user/out` on our local system.
 
 ### Output derivative structure
 Neuroscout creates a unique output directory `neuroscout-{analysis_id}` for each analysis.
@@ -99,7 +99,7 @@ The resulting cached data directory will look something like this, if you've run
 The next time you run a model with a previously downloaded dataset, it will not need to re-download the fMRI data. </br>
 
 !!! important
-Docker expects **absolute paths** for mounted directories
+    Docker expects **absolute paths** for mounted directories
 
 
 ## Other command line arguments

docs/cli/index.md

@@ -27,13 +27,8 @@ First, check with your HPC administrator that _Singularity_ is available for use
 ### Manually prepared environment
 
 !!! Danger
-    Manually installing _neuroscout-cli_ is not currently recommended. Proceed only if you really need to do this.
+    Manually installing _neuroscout-cli_ can be difficult due to complex dependencies. Proceed only if you really need to do this.
 
 Use pip to install _neuroscout-cli_ directly from the GitHub repo:
 
-    pip install git+https://www.github.com/neuroscout/neuroscout-cli
-
-
-## General usage and reference
-
-Continue [here](usage.md) for a general guide to neuroscout-cli
+    pip install git+https://www.github.com/neuroscout/neuroscout-cli

docs/cli/singularity.md

@@ -42,7 +42,7 @@ This command will download the corresponding preprocessed images, event files an
 The results will be automatically uploaded to NeuroVault, and the analysis page will link to this upload: https://neuroscout.org/builder/Mv3ev.
 
 !!! important
- `neuroscout-cli-<version>.simg` refers to a specific downloaded image on your system. 
+    `neuroscout-cli-<version>.simg` refers to a specific downloaded image on your system. 
 
 
 ## Saving data to disk

docs/cli/usage.md

@@ -84,19 +84,17 @@ Options:
   --help               Show this message and exit.
 ```
 
-The `get` command prepares your system for analysis execution by:
+The `get` command prepares your system for analysis execution by 1) preparing the output directory, 2) downloading the analysis bundle (containing the BIDS StatsModel specification, event files, and more), and 3) downloading the preprocessed fMRI data. 
 
-    1) preparing the output directory
-    1) downloading the analysis bundle (containing the BIDS StatsModel specification, event files, and more configuration)
-    2) downloading the preprocessed fMRI data. Note that only the specific files for that analysis will be download (i.e. only those runs/subjects)
+Note that only the specific files for that analysis will be download (i.e. only those runs/subjects)
 
 By default, the input fMRI data is downloaded to the output directory under `sourcedata`, forming a fully re-executable output.
 However, if you run many analyses with the same dataset, it can be useful to download the data to a common folder that can be re-used in other
 analyses using `--download-dir`
 
 For example:
 
-    ```neuroscout get --download-dir=/home/user/data a54oo /home/user/outputs```
+    neuroscout get --download-dir /home/user/data a54oo /home/user/outputs
 
 In this case, the fMRI dataset will be downloaded to `/home/user/data` and the output folder will be `/home/user/outputs/neuroscout-a54oo`,
 with the bundle contents saved in the output folder.
@@ -108,6 +106,7 @@ with the bundle contents saved in the output folder.
 
 ### Upload
 
+```
 Usage: neuroscout upload [OPTIONS] ANALYSIS_ID OUT_DIR
 
   Upload results.
@@ -121,6 +120,7 @@ Options:
   --no-upload           Don't upload results to NeuroVault
   --upload-first-level  Upload first-level results, in addition to group
   --help                Show this message and exit.
+```
 
 The `upload` command may be useful in case the `run` command experienced an error uploading results,
 particularly if there was a connection error, and you wish to try again. 

mkdocs.yml

@@ -17,7 +17,9 @@ nav:
       - Clone: browse/clone.md
     - Running analyses:
       - Introduction: cli/index.md
-      - Usage: cli/usage.md
+      - Docker: cli/docker.md
+      - Singularity: cli/singularity.md
+      - General Usage: cli/usage.md
     - FAQ: faq.md
 
 theme: readthedocs

neuroscout/frontend/src/analysis_builder/Status.tsx

@@ -268,7 +268,7 @@ export class StatusTab extends React.Component<submitProps, statusTabState> {
               <code>
                 docker run --rm -it -v /local/outputdirectory:/out
                 {` neuroscout/neuroscout-cli${this.state.imageVersion}`} run
-                /out {this.props.analysisId}
+                {this.props.analysisId} /out
               </code>
             </pre>
             <Card