So the travis CI wasn't actually running the tests.

Tests were failing if run as root because there was a test for exception
being thrown in case of being asked to read an inaccessible file,
but when runa s root the file was always accessible so this test
always failed.  Added workaround that skips the test if run as root.
=> added tests into travis script (and Dockerfile)

Dockerfile

@@ -51,3 +51,6 @@ ENV PERL5LIB /opt/Bio-ENA-DataSubmission/lib:$PERL5LIB
 ENV ENA_SUBMISSIONS_DATA /opt/Bio-ENA-DataSubmission/data
 RUN cd /opt/Bio-ENA-DataSubmission && dzil authordeps --missing | cpanm --notest
 RUN cd /opt/Bio-ENA-DataSubmission && dzil listdeps --missing | grep -v 'VRTrack::Lane' | cpanm --notest
+
+RUN   cd /opt/Bio-ENA-DataSubmission && \
+      dzil test

install-travis-dependencies.sh

@@ -30,5 +30,7 @@ cd $start_dir
 dzil authordeps --missing | cpanm --notest
 dzil listdeps --missing | grep -v 'VRTrack::Lane' | cpanm --notest
 
+dzil test
+
 set +eu
 set +x

t/Bio/ENA/DataSubmission/WEBINCli.t

@@ -188,11 +188,15 @@ sub test_directory_not_a_directory {
 
 # Check manifest validation when file is not readable
 {
-    my $args = { %full_args };
-    $args->{'manifest'} = $unreadable_manifest;
-    my $under_test = Bio::ENA::DataSubmission::WEBINCli->new(%$args);
-    throws_ok {$under_test->run()} 'Bio::ENA::DataSubmission::Exception::CannotReadFile', "dies if manifest is not a readable file";
-
+   SKIP: {
+      skip "running as root, so disabled the test \"Check manifest validation when file is not readable\"", 1
+         if ('root' eq scalar(getpwuid $>));
+
+      my $args = { %full_args };
+      $args->{'manifest'} = $unreadable_manifest;
+      my $under_test = Bio::ENA::DataSubmission::WEBINCli->new(%$args);
+      throws_ok {$under_test->run()} 'Bio::ENA::DataSubmission::Exception::CannotReadFile', "dies if manifest is not a readable file";
+   }
 }
 
 remove_tree($temp_input_dir_name, $temp_output_dir_name, $filename, $manifest_filename, $temp_dir_name, $unreadable_manifest);