From aca9490d899a26a535c395a4cd8003e967567b44 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 10 Dec 2019 23:21:29 +0000
Subject: [PATCH] Explicitly include PyPI as an ``--extra-index-url`` to pip

Backport combining commits 244fc834cd4dd3980cc3edb755d22ca5a9372421 and
09fdac513d59ca6dad440616a53daa97751ff905 . This is now needed because
wheels.galaxyproject.org is not a full-fledged pypiserver any more but
just an S3 bucket served via a CDN.
---
 scripts/common_startup.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index 71bb77ae7c9..033e41d2c32 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -130,17 +130,18 @@ if [ $SET_VENV -eq 1 ]; then
 fi
 
 : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
+: ${PYPI_INDEX_URL:="https://pypi.python.org/simple"}
 if [ $REPLACE_PIP -eq 1 ]; then
     pip install 'pip>=8.1'
 fi
 
 if [ $FETCH_WHEELS -eq 1 ]; then
-    pip install -r requirements.txt --index-url ${GALAXY_WHEELS_INDEX_URL}
+    pip install -r requirements.txt --index-url ${GALAXY_WHEELS_INDEX_URL} --extra-index-url "${PYPI_INDEX_URL}"
     GALAXY_CONDITIONAL_DEPENDENCIES=`PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))"`
     [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url ${GALAXY_WHEELS_INDEX_URL}
 fi
 
 if [ $FETCH_WHEELS -eq 1 -a $DEV_WHEELS -eq 1 ]; then
     dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt'
-    [ -f $dev_requirements ] && pip install -r $dev_requirements --index-url ${GALAXY_WHEELS_INDEX_URL}
+    [ -f $dev_requirements ] && pip install -r $dev_requirements --index-url ${GALAXY_WHEELS_INDEX_URL} --extra-index-url "${PYPI_INDEX_URL}"
 fi