From 940d3f583e27528cb3c702fab5867fb3a0223e54 Mon Sep 17 00:00:00 2001 From: Bryan Brancotte <bryan.brancotte@pasteur.fr> Date: Wed, 22 Nov 2023 10:49:14 +0100 Subject: [PATCH] indicate how to run jass with only test data, plus link to how to generate data from docker-compose run section --- doc/source/data_import.rst | 2 ++ doc/source/install.rst | 11 ++++++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/doc/source/data_import.rst b/doc/source/data_import.rst index 8953ca7e..00aa2d3e 100644 --- a/doc/source/data_import.rst +++ b/doc/source/data_import.rst @@ -84,6 +84,8 @@ The init table generation is performed using JASS with the previously-mentionned # import GWAS data into JASS jass create-inittable --input-data-path "GWAS/*.txt" --init-covariance-path "COV.txt" --regions-map-path "regions.txt" --description-file-path "description.txt" --init-table-path "inittable.hdf5" +.. _Create initTable: + How to generate input data for JASS ----------------------------------- diff --git a/doc/source/install.rst b/doc/source/install.rst index 23328fc9..f01b1567 100644 --- a/doc/source/install.rst +++ b/doc/source/install.rst @@ -113,7 +113,7 @@ If using docker-compose is not an option, you need to launch two servers in two Launching with docker compose (recommended) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Once docker and docker-compose installed, just run +Once docker and docker-compose installed, copy the :ref:`initTable.hdf5 you created <Create initTable>` in data/ folder and then run .. code-block:: shell @@ -123,6 +123,15 @@ Once docker and docker-compose installed, just run docker-compose up # then visit http://0.0.0.0:3000/ +If you just want to try jass with test data (i.e without creating an initTable), run: + +.. code-block:: shell + + # build the application + docker-compose build + # launch the whole application with + docker-compose -f docker-compose.yaml -f docker-compose.test.yaml up + # then visit http://0.0.0.0:3000/ launching the two servers on Linux ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- GitLab