setup: prepare for Guix runtime

3 files changed, 28 insertions, 10 deletions

diff --git a/MANIFEST.in b/MANIFEST.in
index f4ea2316..bf23f9aa 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -17,10 +17,6 @@ include wqflask/wqflask/templates/new_security/*
 include wqflask/wqflask/correlation/*
 include wqflask/wqflask/interval_mapping/*
 include wqflask/wqflask/interval_analyst/*
-include wqflask/wqflask/my_pylmm/*
-include wqflask/wqflask/my_pylmm/scripts/*
-include wqflask/wqflask/my_pylmm/pyLMM/*
-include wqflask/wqflask/my_pylmm/data/*
 include wqflask/wqflask/static/*
 include wqflask/wqflask/static/dbdoc/*
 include wqflask/wqflask/static/new/*
@@ -260,3 +256,4 @@ include wqflask/flask_security/templates/security/email/*
 include wqflask/dbFunction/*
 include wqflask/basicStatistics/*
 include wqflask/base/*
+include etc/*.py
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 00ee09bf..e5f04ee1 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,6 +1,9 @@
 #! /bin/bash
 #
-# This will run the server with default settings.
+# This will run the GN2 server (with default settings if none supplied).
+#
+# Environment settings can be used to preconfigure as well as a
+# settings.py file.
 
 # Absolute path to this script, e.g. /home/user/bin/foo.sh
 SCRIPT=$(readlink -f "$0")
@@ -8,20 +11,29 @@ SCRIPT=$(readlink -f "$0")
 GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT"))
 echo $GN2_BASE_PATH
 
+# Handle setting parameter
 settings=$1
 if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi
-export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH
+if [ ! -e $settings ]; then
+    echo "ERROR: can not load settings file $settings"
+    exit 1
+fi
 export WQFLASK_SETTINGS=$settings
 
+# We may change this one:
+export PYTHONPATH=$GN2_BASE_PATH/wqflask:$PYTHONPATH
+
+# TEMPDIR defaults to /tmp if nothing else
 if [ -z $TEMPDIR ]; then
     TEMPDIR="/tmp"
 fi
                          
-# start the redis server
+# Start the redis server
 echo -n "dir $TEMPDIR
 dbfilename gn2.rdb
 " | redis-server - &
 
+# Start the flask server running GN2
 cd $GN2_BASE_PATH/wqflask
 echo "Starting with $settings"
 /usr/bin/env python runserver.py
diff --git a/setup.py b/setup.py
index 1b11acc0..a9b71fab 100755
--- a/setup.py
+++ b/setup.py
@@ -1,8 +1,17 @@
+# Run setup from python - this script is used by the GNU Guix builder.
+
 from setuptools import setup, find_packages
 
 setup(name='genenetwork2',
       version='2.0',
+      author = "The GeneNetwork Team",
+      author_email='rwilliams@uthsc.edu',
+      url = "https://github.com/genenetwork/genenetwork2/blob/master/README.md",
+      description = 'Website and tools for genetics.',
       include_package_data=True,
-      # packages=find_packages()
-      packages=['wqflask']
-      )
+      packages=['wqflask','etc'],
+      scripts=['bin/genenetwork2'],
+      # package_data = {
+      #   'etc': ['*.py']
+      # }
+)