Merge pull request #47 from molssi-seamm/dev

Improving Docker installation documentation

Author: seamm

docs/getting_started/installation/Dashboard.zip

@@ -22,34 +22,22 @@ it easier to start in the future.
 Running this multiple times will do nothing if the Dashboard and JobServer are already
 running. If the are stopped, it will start them.
 
-Linux
------
-You can make an alias in your shell to start the SEAMM GUI. Add the following line to
-your `~/.bashrc` file::
-
-  alias Dashboard='docker compose --file seamm-environment.yaml up -d'
+.. Note::
+   The Dashboard and JobServer are running in Docker, and you can see their status in the
+   Docker Desktop window.
 
-You can then start the Dashboard and Jobserver by typing *Dashboard* in a terminal window.
-
-Windows
--------
-You can make a shortcut to start the Dashboard and JobServer. Right-click on the desktop and select
-"New" and then "Shortcut". In the dialog box that appears, enter the following command::
-
-  C:\Windows\System32\wsl.exe -d docker-desktop -u root -- docker compose --file seamm-environment.yaml up -d
-
-You can then double-click on the shortcut to start the Dashboard and Jobserver.
+.. image:: images/docker-desktop.png
+   :alt: Docker Desktop
 
-.. Warning::
-   We have not yet installed on SEAMM on Windows using Docker. We are working on this!
-   Hopefully the above instruction will work, but we have not tested it yet.
+.. Note::
+   This completes the installation on MacOS.
 
 General
 -------
 .. Important::
    The directory ~/SEAMM needs to exist! If it doesn't, please create it!
 
-Once you have *Docker* installer, you can start the SEAMM environment by running the
+Once you have *Docker* installed, you can start the SEAMM environment by running the
 following command in the terminal::
 
   docker compose --file seamm-environment.yaml up -d
@@ -113,5 +101,31 @@ You should see output like this::
 The Dashboard and JobServer should now be running. You can check the Dashboard at
 http://localhost:55055, and also can use the Docker Desktop window to see their status:
 
+Linux
+-----
+.. Warning::
+   We have not yet installed on SEAMM on Linux using Docker. We are working on this!
+   Hopefully these instructions will work, but we have not tested it yet.
+   
+You can make an alias in your shell to start the SEAMM GUI. Add the following line to
+your `~/.bashrc` file::
+
+  alias Dashboard='docker compose --file seamm-environment.yaml up -d'
+
+You can then start the Dashboard and Jobserver by typing *Dashboard* in a terminal window.
+
+Windows
+-------
+.. Warning::
+   We have not yet installed on SEAMM on Windows using Docker. We are working on this!
+   Hopefully these instructions will work, but we have not tested it yet.
+
+You can make a shortcut to start the Dashboard and JobServer. Right-click on the desktop and select
+"New" and then "Shortcut". In the dialog box that appears, enter the following command::
+
+  C:\Windows\System32\wsl.exe -d docker-desktop -u root -- docker compose --file seamm-environment.yaml up -d
+
+You can then double-click on the shortcut to start the Dashboard and Jobserver.
+
 .. image:: images/docker-desktop.png
    :alt: Docker Desktop

docs/getting_started/installation/SEAMM.zip

@@ -12,7 +12,7 @@ MacOS
 -----
 If you are using MacOS you can install an application for the SEAMM
 GUI. Download :download:`SEAMM.zip <./SEAMM.zip>` and unzip it in your personal
-Applications folder -- the one insde your home directory. You can do this in Finder by
+Applications folder -- the one inside your home directory. You can do this in Finder by
 dragging the file to the Applications directory under your home folder. Then
 double-click on SEAMM.zip to expand it, creating SEAMM.app. You can then double-click on
 SEAMM.app to start the SEAMM GUI. You can also drag the SEAMM.app to your dock to make
@@ -33,19 +33,46 @@ it easier to start in the future.
 
    You will need to do this each time you start *XQuartz*. If you want it to run
    automatically, add a line with *xhost + 127.0.0.1* to the file
-   `~/.xinitrc.d/50-xhost.sh`. You may need to create the directory and file.
+   `~/.xinitrc.d/50-xhost.sh`. You may need to create both the directory and file.
+
+.. Note:
+   If you want to run SEAMM from a terminal window, you can make an alias to start the
+   SEAMM GUI. Add the following line to your `~/.bashrc` file::
+
+     seamm='~/Applications/SEAMM.app/Contents/MacOS/SEAMM'
+
+   You can then start the SEAMM GUI by typing *seamm* in a terminal window. You can also
+   add a flowchart file to open by adding the name of the file to the command line, but
+   it must be in the current directory or below, and you must use a relative path.
 
 Linux
 -----
-You can make an alias in your shell to start the SEAMM GUI. Add the following line to
+.. Warning:
+   The SEAMM installation using Docker on Linux has not yet been thoroughly tested. If
+   you run into problems, please contact us! It will help us to improve the installation
+   and find out if there are differences between different versions of Linux.
+
+   Also, you may need to run `xhost + local:` or `xhost + 127.0.0.1` to allow the SEAMM
+   GUI to connect to the X server. You can add this to your `~/.bashrc` file to run it
+   automatically each time you start a terminal window.
+   
+You can make these aliases in your shell to start the SEAMM GUI. Add the following line to
 your `~/.bashrc` file::
 
-  alias SEAMM='docker run --pull always --rm --name SEAMM --env "DISPLAY=host.docker.internal:0" --network seamm-network -v ~/SEAMM:/root/SEAMM -v ~/.seamm.d:/root/.seamm.d ghcr.io/molssi-seamm/seamm:latest &'
+  alias seamm-standalone='docker run --pull always -v /tmp/.X11-unix/:/root/.X11-unix/ --net=host --rm --name SEAMM --env "DISPLAY" -v ~/SEAMM:/root/SEAMM -v ~/.seamm.d:/root/.seamm.d ghcr.io/molssi-seamm/seamm:latest &'
+  alias seamm='docker run --pull always -v /tmp/.X11-unix/:/root/.X11-unix/ --net=host --network seamm-netowrk --rm --name SEAMM --env "DISPLAY" -v ~/SEAMM:/root/SEAMM -v ~/.seamm.d:/root/.seamm.d ghcr.io/molssi-seamm/seamm:latest &'
 
-You can then start the SEAMM GUI by typing *SEAMM* in a terminal window.
+You can then start the SEAMM GUI by typing *seamm-standalone* or *seamm* in a terminal
+window. The standalone version can only connect to Dashboards on other machines. If you
+are running the SEAMM Dashboard locally, using Docker, and want to access it, you will
+need the second version, *seamm*.
 
 Windows
 -------
+.. Warning:
+   We have not tested the SEAMM installation using Docker on Windows. If you run into
+   problems, please contact us!
+   
 You can make a shortcut to start the SEAMM GUI. Right-click on the desktop and select
 "New" and then "Shortcut". In the dialog box that appears, enter the following command::
 
@@ -58,17 +85,4 @@ You can then double-click on the shortcut to start the SEAMM GUI.
    We have not yet installed on SEAMM on Windows using Docker. We are working on this!
    Hopefully the above instruction will work, but we have not tested it yet.
 
-General
--------
-Once you have *Docker* installed, you can start the SEAMM GUI by running the following
-command in a terminal window::
-
-  docker run --pull always --rm --name SEAMM \
-		      --env "DISPLAY=host.docker.internal:0" \
-		      --network seamm-network \
-		      -v ~/SEAMM:/root/SEAMM \
-		      -v ~/.seamm.d:/root/.seamm.d \
-		      ghcr.io/molssi-seamm/seamm:latest &
-
-
 .. _XQuartz: https://www.xquartz.org