diff --git a/scripts/travis_install.sh b/scripts/travis_install.sh
index c73a08a61..50c815cf9 100755
--- a/scripts/travis_install.sh
+++ b/scripts/travis_install.sh
@@ -2,6 +2,10 @@
 
 set -e -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}
+
 sudo apt-get install -qq odbc-postgresql
 sudo apt-get install libgd2-xpm-dev # For npg_tracking
 sudo apt-get install liblzma-dev # For npg_qc
@@ -65,11 +69,13 @@ cpanm --quiet --notest Module::Build
 # WTSI NPG Perl repo dependencies
 repos=""
 for repo in perl-dnap-utilities perl-irods-wrap ml_warehouse npg_ml_warehouse npg_tracking npg_seq_common npg_qc; do
-  cd /tmp
-  git clone --branch master --depth 1 ${WTSI_NPG_GITHUB_URL}/${repo}.git ${repo}.git #always clone master when using depth 1 to get current tag
-  cd /tmp/${repo}.git
-  git pull origin ${TRAVIS_BRANCH} || echo 'so, staying on master branch....' #shift off master to appropriate branch (if possible)
-  repos=$repos" /tmp/${repo}.git" 
+    cd /tmp
+    # Always clone master when using depth 1 to get current tag
+    git clone --branch master --depth 1 ${WTSI_NPG_GITHUB_URL}/${repo}.git ${repo}.git
+    cd /tmp/${repo}.git
+    # Shift off master to appropriate branch (if possible)
+    git ls-remote --heads --exit-code origin ${WTSI_NPG_BUILD_BRANCH} && git pull origin ${WTSI_NPG_BUILD_BRANCH} && echo "Switched to branch ${WTSI_NPG_BUILD_BRANCH}"
+    repos=$repos" /tmp/${repo}.git"
 done
 
 # Install CPAN dependencies. The src libs are on PERL5LIB because of