diff --git a/docs/index.rst b/docs/index.rst index 64d0440c..08143e36 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -18,6 +18,7 @@ Contents: usage/installation usage/quick_rule usage/snakemake_docs + usage/faq .. toctree:: :maxdepth: 2 diff --git a/docs/usage/faq.rst b/docs/usage/faq.rst new file mode 100644 index 00000000..03a4ca98 --- /dev/null +++ b/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.