Description: drop some use of FindBin and hardcode paths
Author: Tim Booth <tbooth@ceh.ac.uk>
--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
+++ trinityrnaseq/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
@@ -8,7 +8,7 @@
 use FindBin;
 use File::Basename;
 
-$ENV{PATH} .= ":$FindBin::RealBin/../../trinity-plugins/slclust/bin/";
+$ENV{PATH} .= ":/usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/";
 
 my $help_flag;
 
--- trinityrnaseq.orig/Trinity
+++ trinityrnaseq/Trinity
@@ -5,8 +5,7 @@
 use threads;
 no strict qw(subs refs);
 
-use FindBin;
-use lib ("$FindBin::RealBin/PerlLib");
+use lib ("/usr/lib/trinityrnaseq/PerlLib");
 use File::Basename;
 use Time::localtime;
 use Cwd;
@@ -23,7 +22,7 @@
 
 BEGIN {
 
-    $ENV{TRINITY_HOME} = "$FindBin::RealBin";
+    $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
 
 }
 
@@ -446,7 +445,7 @@
 #        Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
 #                --genome_guided_max_intron 10000 --CPU 6
 #
-#     see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
+#     see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
 #          for sample data and 'runMe.sh' for example Trinity execution
 #
 #     For more details, visit: http://trinityrnaseq.github.io
--- trinityrnaseq.orig/util/align_and_estimate_abundance.pl
+++ trinityrnaseq/util/align_and_estimate_abundance.pl
@@ -2,7 +2,6 @@
 
 use strict;
 use warnings;
-use FindBin;
 
 use Cwd;
 use Carp;
@@ -426,7 +425,7 @@
 
     if ($trinity_mode && ! $gene_trans_map_file) {
         $gene_trans_map_file = "$transcripts.gene_trans_map";
-        my $cmd = "$FindBin::RealBin/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file";
+        my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/get_Trinity_gene_to_trans_map.pl $transcripts > $gene_trans_map_file";
         &process_cmd($cmd) unless (-e $gene_trans_map_file);
     }
 
@@ -698,7 +697,7 @@
     
     if ($gene_trans_map_file) {
         
-        my $cmd = "$FindBin::RealBin/support_scripts/eXpress_trans_to_gene_results.pl results.xprs $gene_trans_map_file > results.xprs.genes";
+        my $cmd = "/usr/lib/trinityrnaseq/util/support_scripts/eXpress_trans_to_gene_results.pl results.xprs $gene_trans_map_file > results.xprs.genes";
         &process_cmd($cmd);
     }
     
@@ -873,7 +872,7 @@
         
         if ($gene_trans_map_file) {
             
-            my $cmd = "$FindBin::RealBin/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes";
+            my $cmd = "/usr/lib/trinityrnaseq/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes";
             &process_cmd($cmd);
         }
     }
@@ -960,7 +959,7 @@
         
         if ($gene_trans_map_file) {
             
-            my $cmd = "$FindBin::RealBin/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes";
+            my $cmd = "/usr/lib/trinityrnaseq/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes";
             &process_cmd($cmd);
         }
     }
