From cd225e8d3f9efec01e9cadcf8934865e5add39dd Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Tue, 17 Mar 2020 12:53:47 +0000
Subject: [PATCH 1/4] Use environment variables for config path

---
 lib/Pathogens/ConfigSettings.pm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/Pathogens/ConfigSettings.pm b/lib/Pathogens/ConfigSettings.pm
index e45ce74..6c55b03 100644
--- 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;
 } 
 

From 98f6ad3ce330b58ff888de2e0a3f675966dbbb90 Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Tue, 17 Mar 2020 15:19:01 +0000
Subject: [PATCH 2/4] fixing apt dependency required by a perl package

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index e7d8a46..6f4c187 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,6 +5,7 @@ addons:
     - libmysqlclient-dev
     - autoconf
     - libtool
+    - libdb-dev
 perl:
   - 5.14
 services:

From f408b2e008d1bdd4f7787c24a5621d55efea392f Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Tue, 17 Mar 2020 16:26:24 +0000
Subject: [PATCH 3/4] Try to fix perl dependency

---
 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 6f4c187..982f422 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,6 +6,10 @@ addons:
     - autoconf
     - libtool
     - libdb-dev
+    - build-essential
+    - libssl-dev
+    - libexpat1-dev
+    - libdbd-mysql-perl
 perl:
   - 5.14
 services:

From c6a2e76d706fc36037d5c0d46831d50b98f1a097 Mon Sep 17 00:00:00 2001
From: Olivier Seret <os7@sanger.ac.uk>
Date: Tue, 17 Mar 2020 16:27:37 +0000
Subject: [PATCH 4/4] Try to fix perl dependency

---
 install_dependencies.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/install_dependencies.sh b/install_dependencies.sh
index 0bc7262..5bd2657 100755
--- 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
\ No newline at end of file
+set +x