Update installation instructions

docs/usage/installation.rst

@@ -1,54 +1,115 @@
 Installation
 ===============
 
-This instructions have been tested on MacOS Cataline and Ubuntu 16.04. If you find a problem, please report it.
+This instructions have been tested on MacOS Catalina and Ubuntu 16.04. If you find a problem, please report it.
 
-Install MySQL
+Mac OS (tested on Catalina)
+----------------------------
 
-- ``brew install mysql``
+#. Install MySQL
-- ``brew services start mysql``
 
-Install R and rmarkdown:
+    - ``brew install mysql``
+    - ``brew services start mysql``
 
-- ``brew install r``
+#. Install R, pandoc and rmarkdown:
-- ``brew install pandoc``
-- ``R -e 'install.packages(c( "rmarkdown"))'``
 
-Install miniconda:
+    - ``brew install r``
+    - ``brew install pandoc``
+    - ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
 
-For Mac:
+#. Install miniconda:
+    - ``brew cask install miniconda``
+    - ``conda init zsh`` or ``conda init bash``
+    - Restart terminal if necessary
 
-- ``brew cask install miniconda``
+#. Clone our repo:
-- ``conda init zsh`` or - ``conda init bash``
-	
-Clone our repo:
 
-- ``git clone https://github.com/carissalow/moshi-aware-pipeline``
+    - ``git clone https://github.com/carissalow/moshi-aware-pipeline``
 
-Create a python virtual environment:
+#. Create a python virtual environment:
 
-- ``conda env create -f environment.yml``
+    - ``conda env create -f environment.yml -n MY_ENV_NAME``
-- Restart terminal if necessary
+    - ``conda activate MY_ENV_NAME``
-- ``conda activate moshi-env``
 
-Install r packages and virtual environment:
+#. Install r packages and virtual environment:
 
-- ``snakemake packrat_install``
+    - ``snakemake packrat_install``
-- ``snakemake packrat_init``
+    - ``snakemake packrat_init``
-- ``snakemake packrat_restore``
+    - ``snakemake packrat_restore``
 
-Configure the participants to analyze:
+#. Configure the participants to analyze:
 
-- Add a file per participant and name it with the label for that participant, no extension is necessary: ``/data/external/pxx``
+    - Create a file per participant in the ``/data/external`` folder, no extension is necessary, its name will be the label for that participant in the pipeline: ``/data/external/pxx``
-- Add a line with the device_id for that participant as it appears on the db
+    - Add a line with the device_id(s) of that participant as it appears on the database. If multiple device ids, all data for this participant will be relabeled with the last one
-- Add a line with the mobile platform (Android, or iOS)
+    - Add a line with the mobile platform (android, or ios)
+    - For example:
+        .. code-block:: bash
 
-Configure the db connection:
+            3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
+            android
 
-- Create an empty .env file in the root folder
+#. Configure the db connection:
-- Add and complete the following lines
+
-    | ``[MY_GROUP_NAME]``
+    - Create an empty .env file in the root folder
-    | ``user=MyUSER``
+    - Add and complete the following lines
-    | ``password=MyPassword``
+        | ``[MY_GROUP_NAME]``
-    | ``host=MyIP``
+        | ``user=MyUSER``
-    | ``port=3306``
+        | ``password=MyPassword``
+        | ``host=MyIP``
+        | ``port=3306``
+
+Linux (tested on Ubuntu 16.04)
+------------------------------
+
+#. Install MySQL
+
+    - ``brew install mysql``
+    - ``brew services start mysql``
+
+#. Install R, pandoc and rmarkdown:
+
+    - ``brew install r``
+    - ``brew install gcc@6`` (needed due to this bug_)
+    - ``HOMEBREW_CC=gcc-6 brew install pandoc``
+    - ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
+
+#. Install miniconda using these instructions_
+
+#. Clone our repo:
+
+    - ``git clone https://github.com/carissalow/moshi-aware-pipeline``
+
+#. Create a python virtual environment:
+
+    - ``conda env create -f environment.yml -n MY_ENV_NAME``
+    - ``conda activate MY_ENV_NAME``
+
+#. Install r packages and virtual environment:
+
+    - ``snakemake packrat_install``
+    - ``snakemake packrat_init``
+    - ``snakemake packrat_restore``
+
+#. Configure the participants to analyze:
+
+    - Create a file per participant in the ``/data/external`` folder, no extension is necessary, its name will be the label for that participant in the pipeline: ``/data/external/pxx``
+    - Add a line with the device_id(s) of that participant as it appears on the database. If multiple device ids, all data for this participant will be relabeled with the last one
+    - Add a line with the mobile platform (android, or ios)
+    - For example:
+        .. code-block:: bash
+
+            3a7b0d0a-a9ce-4059-ab98-93a7b189da8a,44f20139-50cc-4b13-bdde-0d5a3889e8f9
+            android
+
+#. Configure the db connection:
+
+    - Create an empty .env file in the root folder
+    - Add and complete the following lines
+        | ``[MY_GROUP_NAME]``
+        | ``user=MyUSER``
+        | ``password=MyPassword``
+        | ``host=MyIP``
+        | ``port=3306``
+
+.. _bug: https://github.com/Homebrew/linuxbrew-core/issues/17812
+.. _instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html