tweak docs

sphinx/_static/css/custom.css

@@ -82,3 +82,7 @@ code.docutils.literal.notranslate {
 #solosis-cli h4 {
   margin-top: 40px;
 }
+
+h1 {
+  font-size: 225%;
+}

sphinx/development.rst

@@ -48,6 +48,14 @@ Set the :code:`PYTHONPATH` environment variable to the :code:`bin` directory whe
 
 .. _pytest: https://docs.pytest.org/en/7.1.x/
 
+.. **Environment Variables**
 
+.. The following environment variables are required to be set for the Solosis module to work correctly.
 
+.. .. code-block:: shell
+..    :caption: Input
+
+..    export TEAM_DATA_DIR="/lustre/scratch126/cellgen/team298/data"
+..    export TEAM_LOGS_DIR="/lustre/scratch126/cellgen/team298/logs"
+..    export LSB_DEFAULT_USERGROUP="team298"
 

sphinx/index.rst

@@ -43,7 +43,7 @@ This tool is made to work with farm22.
 
 
 Quick-start
-===========
+-----------
 3 initial commands to start using solosis.
 
 1. To use Solosis from the Wellcome Sanger Institute, add the module path.

sphinx/setup.rst

@@ -17,35 +17,11 @@ Then load the Solosis module
 
    module load solosis
 
+.. admonition:: Working with iRODS
 
+   If you're running commands that work with iRODS, please load the module and authenticate yourself.
 
-**Environment Variables**
+   .. code-block:: shell
 
-Then load environment variables 
-
-.. code-block:: shell
-   :caption: Input
-
-   export TEAM_DATA_DIR=/lustre/scratch126/cellgen/team298/data
-   
-   #change `<YOURGROUP>` to group id (e.g. team298)
-   export LSB_DEFAULT_USERGROUP=<YOURGROUP>
-
-
-
-**iRODS**
-
-For commands using irods, Load the irods module 
-
-.. code-block:: shell
-   :caption: Input
-
-   module load cellgen/irods
-
-
-Then log into irods
-
-.. code-block:: shell
-   :caption: Input
-
-   iinit 
+      module load cellgen/irods
+      iinit