Merge pull request #111 from sanger-pathogens/farm5

Farm5
sanger-pathogens · Mar 17, 2020 · 134bd87 · 134bd87
2 parents dc0b5d4 + c6a2e76
commit 134bd87
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Showing 3 changed files with 13 additions and 6 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -5,6 +5,11 @@ addons:
     - libmysqlclient-dev
     - autoconf
     - libtool
+    - libdb-dev
+    - build-essential
+    - libssl-dev
+    - libexpat1-dev
+    - libdbd-mysql-perl
 perl:
   - 5.14
 services:

diff --git a/install_dependencies.sh b/install_dependencies.sh
@@ -31,13 +31,13 @@ sudo make install
 
 cd $start_dir
 
-cpanm Dist::Zilla
-dzil authordeps --missing | cpanm
-dzil listdeps | cpanm
-cpanm File::Slurp DBI XML::TreePP Bio::DB::EUtilities Parallel::ForkManager Spreadsheet::ParseExcel Test::MockObject Time::Format DBD::mysql YAML::XS IO::Capture::Stderr
+cpanm --notest Dist::Zilla
+dzil authordeps --missing | cpanm --notest
+dzil listdeps | cpanm --notest
+cpanm --notest File::Slurp DBI XML::TreePP Bio::DB::EUtilities Parallel::ForkManager Spreadsheet::ParseExcel Test::MockObject Time::Format DBD::mysql YAML::XS IO::Capture::Stderr
 export LD_LIBRARY_PATH=/usr/local/lib
 
 #Template
 
 set +eu
-set +x
+set +x
diff --git a/lib/Pathogens/ConfigSettings.pm b/lib/Pathogens/ConfigSettings.pm
@@ -20,7 +20,9 @@ has 'settings' => ( is => 'rw', isa => 'HashRef', lazy_build => 1 );
 sub _build_settings 
 {
   my $self = shift;
-  my %config_settings = %{ Load( scalar read_file("config/".$self->environment."/".$self->filename.""))};
+  my $directory = (defined $ENV{'UPDATE_PIPELINE_CONFIG_PATH'}) ? $ENV{'UPDATE_PIPELINE_CONFIG_PATH'} : "config/" . $self->environment ;
+
+  my %config_settings = %{ Load( scalar read_file($directory . "/" . $self->filename.""))};
   return \%config_settings;
 }