Added the FAQ initial documentation pages

docs/index.rst

@@ -18,6 +18,7 @@ Contents:
    usage/installation
    usage/quick_rule
    usage/snakemake_docs
+   usage/faq
 
 .. toctree::
    :maxdepth: 2

docs/usage/faq.rst

@@ -0,0 +1,49 @@
+Frequently Asked Questions 
+============================
+
+1. Cannot connect to the MySQL server
+"""""""""""""""""""""""""""""""""""""""
+**Error in .local(drv, ...) :**
+**Failed to connect to database: Error: Can't initialize character set unknown (path: compiled_in)**
+::
+
+    Calls: dbConnect -> dbConnect -> .local -> .Call
+    Execution halted
+    [Tue Mar 10 19:40:15 2020]
+    Error in rule download_dataset:
+        jobid: 531
+        output: data/raw/p60/locations_raw.csv
+
+    RuleException:
+    CalledProcessError in line 20 of /home/ubuntu/rapids/rules/preprocessing.snakefile:
+    Command 'set -euo pipefail;  Rscript --vanilla /home/ubuntu/rapids/.snakemake/scripts/tmp_2jnvqs7.download_dataset.R' returned non-zero exit status 1.
+    File "/home/ubuntu/rapids/rules/preprocessing.snakefile", line 20, in __rule_download_dataset
+    File "/home/ubuntu/anaconda3/envs/moshi-env/lib/python3.7/concurrent/futures/thread.py", line 57, in run
+    Shutting down, this might take some time.
+    Exiting because a job execution failed. Look above for error message
+
+**Solution:**
+
+Please make sure the ``MY_GROUP`` in ``config.yaml`` and ``.env`` are the same.
+
+2. Cannot start mysql for linux via ``brew services start mysql``
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+use the following code instead:
+
+``mysql.server start``
+
+3. Every time I run ``snakemake -R download_dataset`` all rules are executed
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+This is expected behavior. The advantage of using ``snakemake`` under the hood is that every time a file containing data is modified every rule that depends on that file will be re-executed to update their results. In this case, since ``download_dataset`` updates all the raw data, every single rule that depends on those raw files will be executed.
+
+4. Got an error while running ``snakemake packrat_install`` to setup the RAPIDS environment
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+**Error:**
+::
+
+    SyntaxError in line 19 of /Users/caomz/rapids/Snakefile:
+    Unexpected keyword expand in rule definition (Snakefile, line 19)
+
+**Solution:**
+
+Please make sure there are no extra whitespaces in Snakefile.