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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--
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