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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;
@@ -22,7 +21,7 @@
BEGIN {
- $ENV{TRINITY_HOME} = "$FindBin::RealBin";
+ $ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
}
@@ -445,7 +444,7 @@
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
# --genome_guided_max_intron 10000 --CPU 6
#
-# see: $FindBin::RealBin/sample_data/test_Trinity_Assembly/
+# see: /usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/
# for sample data and 'runMe.sh' for example Trinity execution
#
# For more details, visit: http://trinityrnaseq.github.io
--- trinityrnaseq.orig/util/align_and_estimate_abundance.pl
+++ trinityrnaseq/util/align_and_estimate_abundance.pl
@@ -2,7 +2,6 @@
use strict;
use warnings;
-use FindBin;
use Cwd;
use Carp;
@@ -399,7 +398,7 @@
if ($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 $gene_trans_map_file);
}
@@ -663,7 +662,7 @@
if ($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);
}
@@ -821,7 +820,7 @@
if ( ($left || $single) && $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/util/support_scripts/kallisto_trans_to_gene_results.pl $output_dir/abundance.tsv $gene_trans_map_file > $output_dir/abundance.tsv.genes";
&process_cmd($cmd);
}
@@ -898,7 +897,7 @@
if ( ($left || $single) && $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/util/support_scripts/salmon_trans_to_gene_results.pl $output_dir/quant.sf $gene_trans_map_file > $output_dir/quant.sf.genes";
&process_cmd($cmd);
}
|
