From 5af83433955245ea7e029d7a2410ae52ace08e65 Mon Sep 17 00:00:00 2001
From: Keith James <kdj@sanger.ac.uk>
Date: Tue, 6 Dec 2016 13:09:58 +0000
Subject: [PATCH] Added -u to require initialised variables.

---
 .travis/before_install.sh         | 1 +
 .travis/before_install_mysql57.sh | 2 +-
 .travis/install.sh                | 4 +++-
 .travis/script.sh                 | 2 +-
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.travis/before_install.sh b/.travis/before_install.sh
index 9a9fe1f59..c613965ed 100755
--- a/.travis/before_install.sh
+++ b/.travis/before_install.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
 set -e -x
+# set -u fails cause npm install to fail
 
 sudo apt-get update -qq
 
diff --git a/.travis/before_install_mysql57.sh b/.travis/before_install_mysql57.sh
index 684ea0815..8c0efa32e 100755
--- a/.travis/before_install_mysql57.sh
+++ b/.travis/before_install_mysql57.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e -x
+set -e -u -x
 
 sudo apt-key add ./.travis/mysql_pubkey.asc # Import public key for MySQL
 sudo apt-get remove --purge "^mysql.*"
diff --git a/.travis/install.sh b/.travis/install.sh
index 8d2b72193..bb1d795ff 100755
--- a/.travis/install.sh
+++ b/.travis/install.sh
@@ -8,11 +8,12 @@
 # iRODS setup added by Iain Bancarz (ib5), adapted from baton:
 #   https://github.com/wtsi-npg/baton
 
-set -e -x
+set -e -u -x
 
 # The default build branch for all repositories. This defaults to
 # TRAVIS_BRANCH unless set in the Travis build environment.
 WTSI_NPG_BUILD_BRANCH=${WTSI_NPG_BUILD_BRANCH:=$TRAVIS_BRANCH}
+IRODS_RIP_DIR=${IRODS_RIP_DIR:+$IRODS_RIP_DIR}
 
 sudo apt-get install libgd2-xpm-dev # For npg_tracking
 sudo apt-get install liblzma-dev # For npg_qc
@@ -58,6 +59,7 @@ fi
 sudo ldconfig
 
 # WTSI NPG Perl repo dependencies
+repos=""
 for repo in perl-dnap-utilities ml_warehouse npg_tracking npg_seq_common perl-irods-wrap; do
     cd /tmp
     # Always clone master when using depth 1 to get current tag
diff --git a/.travis/script.sh b/.travis/script.sh
index 0a306574e..b870afc74 100755
--- a/.travis/script.sh
+++ b/.travis/script.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e -x
+set -e -u -x
 
 unset PERL5LIB