From 52e1955a0ec2d12bd6864627e2c4e141bb526418 Mon Sep 17 00:00:00 2001 From: JulioV Date: Fri, 14 Aug 2020 17:59:05 -0400 Subject: [PATCH] Update example.rst --- docs/usage/example.rst | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/docs/usage/example.rst b/docs/usage/example.rst index 1e01146b..4b1547e8 100644 --- a/docs/usage/example.rst +++ b/docs/usage/example.rst @@ -7,14 +7,26 @@ This is a quick guide for creating and running a simple pipeline to analysis an #. Install RAPIDS. See :ref:`Installation Section `. -#. Make sure your database connection credentials in ``.env`` have write permission and set the correct ``MY_GROUP`` parameter in ``config.yaml`` file. See step 1 of :ref:`Usage Section `. +#. Configure your database credentials (see example below or step 1 of :ref:`Usage Section ` for more information). -#. Make sure your Conda (python) environment is active. See step 6 of :ref:`install-page`. + #. Create an ``.env`` file at the root of RAPIDS folder + #. Your MySQL user must have write permissions because we will restore our example database + #. Name your credentials group ``MY_GROUP``. + #. If you are trying to connect to a local MySQL server from our docker container set your host according to this link_. + #. You can name your database anyway you want, for example ``rapids_example`` + + [MY_GROUP] + user=rapids + password=rapids + host=127.0.0.1 # or use host.docker.internal from our docker container + port=3306 + database=rapids_example + +#. Make sure your Conda (python) environment is active (the environment is already active in our docker container). See step 6 of :ref:`install-page`. #. Run the following command to restore database from ``rapids_example.sql`` file:: - sankemake -j1 restore_sql_file - + snakemake -j1 restore_sql_file #. Create example participants files with the following command:: @@ -30,3 +42,4 @@ This is a quick guide for creating and running a simple pipeline to analysis an snakemake -j8 --profile example_profile +.. _link: https://stackoverflow.com/questions/24319662/from-inside-of-a-docker-container-how-do-i-connect-to-the-localhost-of-the-mach