From 00596e663421918ec8e74f5e584d77c84013c90c Mon Sep 17 00:00:00 2001
From: thanhleviet <thanh.le-viet@quadram.ac.uk>
Date: Wed, 4 Dec 2019 13:05:35 +0000
Subject: [PATCH] Remove hardcoded path

---
 bin/add_tradis_tags      | 2 +-
 bin/bacteria_tradis      | 4 ++--
 bin/check_tradis_tags    | 2 +-
 bin/combine_tradis_plots | 2 +-
 bin/filter_tradis_tags   | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/bin/add_tradis_tags b/bin/add_tradis_tags
index d55123f..b4edc08 100755
--- a/bin/add_tradis_tags
+++ b/bin/add_tradis_tags
@@ -14,7 +14,7 @@ Checks the presence of tr/tq tags in a given BAM file
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
 BEGIN { unshift( @INC, "$Bin/../lib/" ) }
 
 use Bio::Tradis::CommandLine::AddTags;
diff --git a/bin/bacteria_tradis b/bin/bacteria_tradis
index 14b801c..abdeb63 100755
--- a/bin/bacteria_tradis
+++ b/bin/bacteria_tradis
@@ -3,7 +3,7 @@
 package Bio::Tradis::Bin::RunTradis;
 
 use FindBin qw($Bin);
-=======
+
 
 
 # ABSTRACT: Perform full tradis analysis
@@ -18,7 +18,7 @@ site plots for use in Artemis
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
 BEGIN { unshift( @INC, "$Bin/../lib/" ) }
 
 use Bio::Tradis::CommandLine::TradisAnalysis;
diff --git a/bin/check_tradis_tags b/bin/check_tradis_tags
index 09733fd..9387442 100755
--- a/bin/check_tradis_tags
+++ b/bin/check_tradis_tags
@@ -14,7 +14,7 @@ Checks the presence of tr/tq tags in a given BAM file
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
 BEGIN { unshift( @INC, "$Bin/../lib/" ) }
 
 use Bio::Tradis::CommandLine::CheckTags;
diff --git a/bin/combine_tradis_plots b/bin/combine_tradis_plots
index d892dd2..ef134bf 100755
--- a/bin/combine_tradis_plots
+++ b/bin/combine_tradis_plots
@@ -17,7 +17,7 @@ plotfile and as an identifier in the stats file, so ensure these are unique.
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
 BEGIN { unshift( @INC, "$Bin/../lib/" ) }
 
 use Bio::Tradis::CommandLine::PlotCombine;
diff --git a/bin/filter_tradis_tags b/bin/filter_tradis_tags
index 180fca5..4b6f725 100755
--- a/bin/filter_tradis_tags
+++ b/bin/filter_tradis_tags
@@ -15,7 +15,7 @@ match the tag provided
 
 BEGIN { unshift( @INC, '../lib' ) }
 BEGIN { unshift( @INC, './lib' ) }
-BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
+# BEGIN { unshift( @INC, '/software/pathogen/internal/prod/lib/' ) }
 BEGIN { unshift( @INC, "$Bin/../lib/" ) }
 
 use Bio::Tradis::CommandLine::FilterFastqTags;