[med-svn] [Git][med-team/trinityrnaseq][master] 4 commits: fix patch error
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Oct 8 18:03:35 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits:
680aad59 by Michael R. Crusoe at 2020-10-08T16:58:38+02:00
fix patch error
- - - - -
6c3955ae by Michael R. Crusoe at 2020-10-08T17:36:36+02:00
Correct location of bamsifter installation
- - - - -
1620ba48 by Michael R. Crusoe at 2020-10-08T17:52:09+02:00
debian/patches/fix_system_paths: fix expected path for ParaFly
- - - - -
6c20b127 by Michael R. Crusoe at 2020-10-08T18:12:12+02:00
debian/patches/update-paths: fix paths to Butterfly.jar
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/bamsifter_build
- debian/patches/fix_system_paths
- debian/patches/series
- debian/patches/update-paths
- debian/trinityrnaseq.install
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
trinityrnaseq (2.11.0+dfsg-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* Fix gcc-10 build issue
Closes: #966876
@@ -10,6 +11,11 @@ trinityrnaseq (2.11.0+dfsg-1) UNRELEASED; urgency=medium
* Remove __pycache__ from installed package
FIXME: seqtk-trinity is missing and thus autopkgtest fails
+ [ Michael R. Crusoe ]
+ * Correct location of bamsifter installation
+ * debian/patches/fix_system_paths: fix expected path for ParaFly
+ * debian/patches/update-paths: fix paths to Butterfly.jar
+
-- Andreas Tille <tille at debian.org> Wed, 05 Aug 2020 12:44:59 +0200
trinityrnaseq (2.10.0+dfsg-1) unstable; urgency=medium
=====================================
debian/patches/bamsifter_build
=====================================
@@ -0,0 +1,23 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Build bamsifter using the system htslib
+Forwarded: not-needed
+--- trinityrnaseq.orig/trinity-plugins/bamsifter/Makefile
++++ trinityrnaseq/trinity-plugins/bamsifter/Makefile
+@@ -1,12 +1,6 @@
++all: bamsifter
++
++bamsifter: sift_bam_max_cov.cpp FORCE
++ $(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=c++11 -o bamsifter sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts
+
+-
+-cwd = $(shell pwd)
+-
+-sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h
+- $(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts
+-
+-
+-htslib/version.h :
+- ./build_htslib.sh
+-
+-
++FORCE:
=====================================
debian/patches/fix_system_paths
=====================================
@@ -1,8 +1,8 @@
Description: drop some use of FindBin and hardcode paths
Author: Tim Booth <tbooth at ceh.ac.uk>
---- a/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
-+++ b/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
-@@ -5,10 +5,9 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
+@@ -5,10 +5,9 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
@@ -14,7 +14,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $help_flag;
-@@ -87,7 +86,7 @@ if ($help_flag) {
+@@ -87,7 +86,7 @@
die $usage;
}
@@ -23,9 +23,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $found_all_tools = 1;
my @required_tools = qw (blat slclust);
---- a/Trinity
-+++ b/Trinity
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -5,8 +5,7 @@
use threads;
no strict qw(subs refs);
@@ -35,7 +35,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Time::localtime;
use Cwd;
-@@ -27,7 +26,7 @@ my $VERSION = "Trinity-v2.11.0";
+@@ -27,7 +26,7 @@
BEGIN {
@@ -44,8 +44,12 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
}
-@@ -38,8 +37,8 @@ open (STDERR, ">&STDOUT"); ## capturing
- my $ROOTDIR = "$FindBin::RealBin";
+@@ -35,16 +34,16 @@
+
+
+ #directory defnintions
+-my $ROOTDIR = "$FindBin::RealBin";
++my $ROOTDIR = "/usr/lib/trinityrnaseq";
my $UTILDIR = "$ROOTDIR/util";
my $MISCDIR = "$UTILDIR/misc";
-my $INCHWORM_DIR = "$ROOTDIR/Inchworm/bin/";
@@ -55,7 +59,13 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/COLLECTL/collectl";
my $TRINITY_PLUGINS_DIR = "$ROOTDIR/trinity-plugins";
-@@ -499,7 +498,7 @@ my $usage_synopsis = qq^#
+ my $TRINITY_BIN_DIR = "$TRINITY_PLUGINS_DIR/BIN";
+-my $PARAFLY = "$TRINITY_BIN_DIR/ParaFly";
++my $PARAFLY = "/usr/bin/ParaFly";
+ my $HTSLIB_DIR = "$ROOTDIR/trinity-plugins/htslib";
+
+ $ENV{LD_LIBRARY_PATH} .= ":${HTSLIB_DIR}";
+@@ -499,7 +498,7 @@
# Trinity --genome_guided_bam rnaseq_alignments.csorted.bam --max_memory 50G\
# --genome_guided_max_intron 10000 --CPU 6
#
@@ -64,8 +74,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
# for sample data and 'runMe.sh' for example Trinity execution
#
# For more details, visit: http://trinityrnaseq.github.io
---- a/util/align_and_estimate_abundance.pl
-+++ b/util/align_and_estimate_abundance.pl
+--- trinityrnaseq.orig/util/align_and_estimate_abundance.pl
++++ trinityrnaseq/util/align_and_estimate_abundance.pl
@@ -2,7 +2,6 @@
use strict;
@@ -74,7 +84,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Cwd;
use Carp;
-@@ -418,7 +417,7 @@ main: {
+@@ -418,7 +417,7 @@
if ($trinity_mode && ! $gene_trans_map_file) {
$gene_trans_map_file = "$transcripts.gene_trans_map";
@@ -83,7 +93,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd) unless (-e $gene_trans_map_file);
}
-@@ -824,7 +823,7 @@ sub run_kallisto {
+@@ -824,7 +823,7 @@
if ($gene_trans_map_file) {
@@ -92,7 +102,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
}
}
-@@ -890,7 +889,7 @@ sub run_salmon {
+@@ -890,7 +889,7 @@
if ($gene_trans_map_file) {
@@ -101,8 +111,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
}
};
---- a/Analysis/DifferentialExpression/ROKU.pl
-+++ b/Analysis/DifferentialExpression/ROKU.pl
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/ROKU.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/ROKU.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -113,9 +123,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use BHStats;
my $usage = "usage: $0 fpkm.matrix\n\n";
---- a/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
-+++ b/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use File::Basename;
@@ -126,7 +136,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use CanvasXpress::Heatmap;
-@@ -80,7 +79,7 @@ main: {
+@@ -80,7 +79,7 @@
open (my $ofh, ">$R_script") or die "Error, cannot write to file $R_script";
@@ -135,8 +145,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "get_cluster_info(\"$R_data_file\")\n";
close $ofh;
---- a/Analysis/DifferentialExpression/get_transcript_lengths.pl
-+++ b/Analysis/DifferentialExpression/get_transcript_lengths.pl
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/get_transcript_lengths.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/get_transcript_lengths.pl
@@ -2,8 +2,7 @@
use strict;
@@ -147,9 +157,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/Analysis/DifferentialExpression/merge_matrices.pl
-+++ b/Analysis/DifferentialExpression/merge_matrices.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/merge_matrices.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/merge_matrices.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
@@ -160,9 +170,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Data::Dumper;
---- a/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
-+++ b/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
@@ -173,9 +183,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Data::Dumper;
---- a/Analysis/DifferentialExpression/run_DE_analysis.pl
-+++ b/Analysis/DifferentialExpression/run_DE_analysis.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/run_DE_analysis.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/run_DE_analysis.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Cwd;
@@ -186,7 +196,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Data::Dumper;
-@@ -442,7 +441,7 @@ sub run_edgeR_sample_pair {
+@@ -442,7 +441,7 @@
print $ofh "write.table(rnaseqMatrix, file=\'$output_prefix.edgeR.count_matrix\', sep='\t', quote=F, row.names=T)\n";
## generate MA and Volcano plots
@@ -195,7 +205,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "pdf(\"$output_prefix.edgeR.DE_results.MA_n_Volcano.pdf\")\n";
print $ofh "plot_MA_and_Volcano(rownames(result_table), result_table\$logCPM, result_table\$logFC, result_table\$FDR)\n";
-@@ -542,7 +541,7 @@ sub run_DESeq2_sample_pair {
+@@ -542,7 +541,7 @@
## generate MA and Volcano plots
@@ -204,7 +214,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "pdf(\"$output_prefix.DESeq2.DE_results.MA_n_Volcano.pdf\")\n";
print $ofh "plot_MA_and_Volcano(rownames(res), log2(res\$baseMean+1), res\$log2FoldChange, res\$padj)\n";
print $ofh "dev.off()\n";
-@@ -621,7 +620,7 @@ sub run_limma_voom_sample_pair {
+@@ -621,7 +620,7 @@
## generate MA and Volcano plots
print $ofh "# MA and volcano plots\n";
@@ -213,7 +223,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "pdf(\"$output_prefix.voom.DE_results.MA_n_Volcano.pdf\")\n";
print $ofh "plot_MA_and_Volcano(rownames(tTags2), tTags2\$logCPM, tTags\$logFC, tTags\$'adj.P.Val')\n";
print $ofh "dev.off()\n";
-@@ -719,7 +718,7 @@ sub run_ROTS_sample_pair {
+@@ -719,7 +718,7 @@
## generate MA and Volcano plots
print $ofh "# MA and volcano plots\n";
@@ -222,9 +232,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "pdf(\"$output_prefix.voom.DE_results.MA_n_Volcano.pdf\")\n";
print $ofh "plot_MA_and_Volcano(rownames(final_table), final_table\$logCPM, final_table\$logFC, final_table\$FDR)\n";
print $ofh "dev.off()\n";
---- a/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
-+++ b/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
@@ -235,7 +245,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Data::Dumper;
-@@ -104,7 +103,6 @@ sub run_TMM {
+@@ -104,7 +103,6 @@
my $tmm_norm_script = "__tmp_runTMM.R";
open (my $ofh, ">$tmm_norm_script") or die "Error, cannot write to $tmm_norm_script";
@@ -243,8 +253,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "library(edgeR)\n\n";
---- a/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
-+++ b/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
++++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
@@ -3,9 +3,8 @@
use strict;
use warnings;
@@ -256,8 +266,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Process_cmd;
---- a/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
-+++ b/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
+--- trinityrnaseq.orig/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
++++ trinityrnaseq/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -268,8 +278,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use WigParser;
---- a/util/misc/ButterflyFastaToGraphDot.pl
-+++ b/util/misc/ButterflyFastaToGraphDot.pl
+--- trinityrnaseq.orig/util/misc/ButterflyFastaToGraphDot.pl
++++ trinityrnaseq/util/misc/ButterflyFastaToGraphDot.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -280,8 +290,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use StringGraph;
---- a/util/misc/HiCpipe_nameSortedSam_to_raw.pl
-+++ b/util/misc/HiCpipe_nameSortedSam_to_raw.pl
+--- trinityrnaseq.orig/util/misc/HiCpipe_nameSortedSam_to_raw.pl
++++ trinityrnaseq/util/misc/HiCpipe_nameSortedSam_to_raw.pl
@@ -3,9 +3,7 @@
use strict;
use warnings;
@@ -293,8 +303,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
use Data::Dumper;
---- a/util/misc/Monarch
-+++ b/util/misc/Monarch
+--- trinityrnaseq.orig/util/misc/Monarch
++++ trinityrnaseq/util/misc/Monarch
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -305,8 +315,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/util/misc/N50.pl
-+++ b/util/misc/N50.pl
+--- trinityrnaseq.orig/util/misc/N50.pl
++++ trinityrnaseq/util/misc/N50.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -317,8 +327,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/util/misc/SAM_coordsorted_max_reads_per_position.pl
-+++ b/util/misc/SAM_coordsorted_max_reads_per_position.pl
+--- trinityrnaseq.orig/util/misc/SAM_coordsorted_max_reads_per_position.pl
++++ trinityrnaseq/util/misc/SAM_coordsorted_max_reads_per_position.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -329,8 +339,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/SAM_intron_extractor.pl
-+++ b/util/misc/SAM_intron_extractor.pl
+--- trinityrnaseq.orig/util/misc/SAM_intron_extractor.pl
++++ trinityrnaseq/util/misc/SAM_intron_extractor.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -341,8 +351,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
-+++ b/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
+--- trinityrnaseq.orig/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
++++ trinityrnaseq/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -353,8 +363,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/SAM_pair_to_bed.pl
-+++ b/util/misc/SAM_pair_to_bed.pl
+--- trinityrnaseq.orig/util/misc/SAM_pair_to_bed.pl
++++ trinityrnaseq/util/misc/SAM_pair_to_bed.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -365,8 +375,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
use Overlap_piler;
---- a/util/misc/SAM_sortAny_to_count_stats.pl
-+++ b/util/misc/SAM_sortAny_to_count_stats.pl
+--- trinityrnaseq.orig/util/misc/SAM_sortAny_to_count_stats.pl
++++ trinityrnaseq/util/misc/SAM_sortAny_to_count_stats.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -377,8 +387,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/SAM_toString.pl
-+++ b/util/misc/SAM_toString.pl
+--- trinityrnaseq.orig/util/misc/SAM_toString.pl
++++ trinityrnaseq/util/misc/SAM_toString.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -389,8 +399,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/SAM_to_bed.pl
-+++ b/util/misc/SAM_to_bed.pl
+--- trinityrnaseq.orig/util/misc/SAM_to_bed.pl
++++ trinityrnaseq/util/misc/SAM_to_bed.pl
@@ -1,10 +1,7 @@
-#!/usr/bin/env perl
-
@@ -403,8 +413,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/SAM_to_fasta.pl
-+++ b/util/misc/SAM_to_fasta.pl
+--- trinityrnaseq.orig/util/misc/SAM_to_fasta.pl
++++ trinityrnaseq/util/misc/SAM_to_fasta.pl
@@ -2,8 +2,7 @@
use strict;
@@ -415,8 +425,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
use Nuc_translator;
---- a/util/misc/allele_simulator.pl
-+++ b/util/misc/allele_simulator.pl
+--- trinityrnaseq.orig/util/misc/allele_simulator.pl
++++ trinityrnaseq/util/misc/allele_simulator.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -427,8 +437,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use List::Util qw(min max);
use Data::Dumper;
---- a/util/misc/average.pl
-+++ b/util/misc/average.pl
+--- trinityrnaseq.orig/util/misc/average.pl
++++ trinityrnaseq/util/misc/average.pl
@@ -2,8 +2,7 @@
use strict;
@@ -439,8 +449,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use BHStats;
my $count = 0;
---- a/util/misc/blast_outfmt6_group_segments.pl
-+++ b/util/misc/blast_outfmt6_group_segments.pl
+--- trinityrnaseq.orig/util/misc/blast_outfmt6_group_segments.pl
++++ trinityrnaseq/util/misc/blast_outfmt6_group_segments.pl
@@ -2,8 +2,7 @@
use strict;
@@ -451,9 +461,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use List::Util qw(min max);
use Overlap_piler;
---- a/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
-+++ b/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
++++ trinityrnaseq/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
+@@ -5,8 +5,7 @@
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -463,8 +473,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Pipeliner;
use File::Basename;
---- a/util/misc/capture_orig_n_unmapped_reads.pl
-+++ b/util/misc/capture_orig_n_unmapped_reads.pl
+--- trinityrnaseq.orig/util/misc/capture_orig_n_unmapped_reads.pl
++++ trinityrnaseq/util/misc/capture_orig_n_unmapped_reads.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -475,9 +485,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Cwd;
use Carp;
---- a/util/misc/cdna_fasta_file_to_transcript_gtf.pl
-+++ b/util/misc/cdna_fasta_file_to_transcript_gtf.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/util/misc/cdna_fasta_file_to_transcript_gtf.pl
++++ trinityrnaseq/util/misc/cdna_fasta_file_to_transcript_gtf.pl
+@@ -4,8 +4,7 @@
use warnings;
@@ -487,8 +497,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/util/misc/check_fastQ_pair_ordering.pl
-+++ b/util/misc/check_fastQ_pair_ordering.pl
+--- trinityrnaseq.orig/util/misc/check_fastQ_pair_ordering.pl
++++ trinityrnaseq/util/misc/check_fastQ_pair_ordering.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -499,8 +509,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
my $usage = "usage: $0 left.fq right.fq\n\n";
---- a/util/misc/contig_ExN50_statistic.pl
-+++ b/util/misc/contig_ExN50_statistic.pl
+--- trinityrnaseq.orig/util/misc/contig_ExN50_statistic.pl
++++ trinityrnaseq/util/misc/contig_ExN50_statistic.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -511,8 +521,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use File::Basename;
---- a/util/misc/ensure_paired_end_bam_file.pl
-+++ b/util/misc/ensure_paired_end_bam_file.pl
+--- trinityrnaseq.orig/util/misc/ensure_paired_end_bam_file.pl
++++ trinityrnaseq/util/misc/ensure_paired_end_bam_file.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -523,9 +533,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/extract_fastQ_pairings.pl
-+++ b/util/misc/extract_fastQ_pairings.pl
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/extract_fastQ_pairings.pl
++++ trinityrnaseq/util/misc/extract_fastQ_pairings.pl
+@@ -5,8 +5,7 @@
use Data::Dumper;
@@ -535,8 +545,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
my $DEBUG = 0;
---- a/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
-+++ b/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
+--- trinityrnaseq.orig/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
++++ trinityrnaseq/util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
@@ -22,8 +22,7 @@
use strict;
use warnings;
@@ -547,8 +557,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
use File::Basename;
---- a/util/misc/fastQ_rand_subset.pl
-+++ b/util/misc/fastQ_rand_subset.pl
+--- trinityrnaseq.orig/util/misc/fastQ_rand_subset.pl
++++ trinityrnaseq/util/misc/fastQ_rand_subset.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -559,8 +569,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
use File::Basename;
---- a/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
-+++ b/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
+--- trinityrnaseq.orig/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
++++ trinityrnaseq/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
@@ -22,8 +22,7 @@
use strict;
use warnings;
@@ -571,8 +581,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
use File::Basename;
---- a/util/misc/fasta_file_reformatter.pl
-+++ b/util/misc/fasta_file_reformatter.pl
+--- trinityrnaseq.orig/util/misc/fasta_file_reformatter.pl
++++ trinityrnaseq/util/misc/fasta_file_reformatter.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -583,8 +593,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 fasta\n";
---- a/util/misc/fasta_filter_by_min_length.pl
-+++ b/util/misc/fasta_filter_by_min_length.pl
+--- trinityrnaseq.orig/util/misc/fasta_filter_by_min_length.pl
++++ trinityrnaseq/util/misc/fasta_filter_by_min_length.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -595,8 +605,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/util/misc/fasta_to_cmd_generator.pl
-+++ b/util/misc/fasta_to_cmd_generator.pl
+--- trinityrnaseq.orig/util/misc/fasta_to_cmd_generator.pl
++++ trinityrnaseq/util/misc/fasta_to_cmd_generator.pl
@@ -1,8 +1,7 @@
#!/usr/bin/env perl
@@ -607,8 +617,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Getopt::Std;
use strict;
---- a/util/misc/fasta_write_sense_n_anti.pl
-+++ b/util/misc/fasta_write_sense_n_anti.pl
+--- trinityrnaseq.orig/util/misc/fasta_write_sense_n_anti.pl
++++ trinityrnaseq/util/misc/fasta_write_sense_n_anti.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -619,8 +629,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Nuc_translator;
---- a/util/misc/fastq_interleave_pairs.pl
-+++ b/util/misc/fastq_interleave_pairs.pl
+--- trinityrnaseq.orig/util/misc/fastq_interleave_pairs.pl
++++ trinityrnaseq/util/misc/fastq_interleave_pairs.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -631,8 +641,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
---- a/util/misc/fastq_unweave_pairs.pl
-+++ b/util/misc/fastq_unweave_pairs.pl
+--- trinityrnaseq.orig/util/misc/fastq_unweave_pairs.pl
++++ trinityrnaseq/util/misc/fastq_unweave_pairs.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -643,8 +653,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
---- a/util/misc/gene_gff3_to_introns.pl
-+++ b/util/misc/gene_gff3_to_introns.pl
+--- trinityrnaseq.orig/util/misc/gene_gff3_to_introns.pl
++++ trinityrnaseq/util/misc/gene_gff3_to_introns.pl
@@ -2,8 +2,7 @@
use strict;
@@ -655,8 +665,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use Fasta_reader;
use GFF3_utils;
---- a/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
-+++ b/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
+--- trinityrnaseq.orig/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
++++ trinityrnaseq/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
@@ -2,8 +2,7 @@
use strict;
@@ -667,8 +677,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
print STDERR "\n\n\tNOTE - longest transcript isn't always the best transcript!... consider filtering based on relative expression support ... \n\n";
---- a/util/misc/gff3_file_to_cdna.pl
-+++ b/util/misc/gff3_file_to_cdna.pl
+--- trinityrnaseq.orig/util/misc/gff3_file_to_cdna.pl
++++ trinityrnaseq/util/misc/gff3_file_to_cdna.pl
@@ -2,8 +2,7 @@
use strict;
@@ -679,8 +689,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use Fasta_reader;
use GFF3_utils;
---- a/util/misc/gff3_file_utr_coverage_trimmer.pl
-+++ b/util/misc/gff3_file_utr_coverage_trimmer.pl
+--- trinityrnaseq.orig/util/misc/gff3_file_utr_coverage_trimmer.pl
++++ trinityrnaseq/util/misc/gff3_file_utr_coverage_trimmer.pl
@@ -2,8 +2,7 @@
use strict;
@@ -691,8 +701,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use Fasta_reader;
use GFF3_utils;
---- a/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
-+++ b/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
+--- trinityrnaseq.orig/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
++++ trinityrnaseq/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -703,8 +713,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use GFF3_utils;
use SAM_reader;
---- a/util/misc/gff3_to_genome_feature_base_encoding.pl
-+++ b/util/misc/gff3_to_genome_feature_base_encoding.pl
+--- trinityrnaseq.orig/util/misc/gff3_to_genome_feature_base_encoding.pl
++++ trinityrnaseq/util/misc/gff3_to_genome_feature_base_encoding.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -715,8 +725,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use GFF3_utils;
use Data::Dumper;
---- a/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
-+++ b/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
+--- trinityrnaseq.orig/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
++++ trinityrnaseq/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -727,8 +737,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use GFF3_alignment_utils;
use WigParser;
use Data::Dumper;
---- a/util/misc/gmap_gff3_to_percent_length_stats.pl
-+++ b/util/misc/gmap_gff3_to_percent_length_stats.pl
+--- trinityrnaseq.orig/util/misc/gmap_gff3_to_percent_length_stats.pl
++++ trinityrnaseq/util/misc/gmap_gff3_to_percent_length_stats.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -739,8 +749,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 gmap.gff3 transcripts.fasta\n\n";
---- a/util/misc/gmap_native_to_format_converter.pl
-+++ b/util/misc/gmap_native_to_format_converter.pl
+--- trinityrnaseq.orig/util/misc/gmap_native_to_format_converter.pl
++++ trinityrnaseq/util/misc/gmap_native_to_format_converter.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -751,8 +761,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
my $usage = "usage: $0 file.gmap (BED|GTF)\n\n";
---- a/util/misc/gtf_to_bed_format.pl
-+++ b/util/misc/gtf_to_bed_format.pl
+--- trinityrnaseq.orig/util/misc/gtf_to_bed_format.pl
++++ trinityrnaseq/util/misc/gtf_to_bed_format.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -763,8 +773,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
my $usage = "usage: $0 transcripts.gtf\n\n";
---- a/util/misc/gtf_to_introns.pl
-+++ b/util/misc/gtf_to_introns.pl
+--- trinityrnaseq.orig/util/misc/gtf_to_introns.pl
++++ trinityrnaseq/util/misc/gtf_to_introns.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -775,8 +785,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use Fasta_reader;
---- a/util/misc/identify_distal_isoform_variations.pl
-+++ b/util/misc/identify_distal_isoform_variations.pl
+--- trinityrnaseq.orig/util/misc/identify_distal_isoform_variations.pl
++++ trinityrnaseq/util/misc/identify_distal_isoform_variations.pl
@@ -2,9 +2,8 @@
use strict;
@@ -788,8 +798,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use GFF3_utils;
---- a/util/misc/illustrate_ref_comparison.pl
-+++ b/util/misc/illustrate_ref_comparison.pl
+--- trinityrnaseq.orig/util/misc/illustrate_ref_comparison.pl
++++ trinityrnaseq/util/misc/illustrate_ref_comparison.pl
@@ -3,9 +3,7 @@
use strict;
use warnings;
@@ -801,8 +811,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Ascii_genome_illustrator;
use Cwd;
---- a/util/misc/jaccard_sam_pair_refiner.pl
-+++ b/util/misc/jaccard_sam_pair_refiner.pl
+--- trinityrnaseq.orig/util/misc/jaccard_sam_pair_refiner.pl
++++ trinityrnaseq/util/misc/jaccard_sam_pair_refiner.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -813,8 +823,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/kmer_counter.pl
-+++ b/util/misc/kmer_counter.pl
+--- trinityrnaseq.orig/util/misc/kmer_counter.pl
++++ trinityrnaseq/util/misc/kmer_counter.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -825,8 +835,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Ktree;
use Nuc_translator;
---- a/util/misc/m8_blastclust.pl
-+++ b/util/misc/m8_blastclust.pl
+--- trinityrnaseq.orig/util/misc/m8_blastclust.pl
++++ trinityrnaseq/util/misc/m8_blastclust.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -837,8 +847,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
---- a/util/misc/map_gtf_transcripts_to_genome_annots.pl
-+++ b/util/misc/map_gtf_transcripts_to_genome_annots.pl
+--- trinityrnaseq.orig/util/misc/map_gtf_transcripts_to_genome_annots.pl
++++ trinityrnaseq/util/misc/map_gtf_transcripts_to_genome_annots.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -849,8 +859,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use GFF3_utils;
use GTF_utils;
---- a/util/misc/merge_blast_n_rsem_results.pl
-+++ b/util/misc/merge_blast_n_rsem_results.pl
+--- trinityrnaseq.orig/util/misc/merge_blast_n_rsem_results.pl
++++ trinityrnaseq/util/misc/merge_blast_n_rsem_results.pl
@@ -2,8 +2,7 @@
use strict;
@@ -861,8 +871,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 rsem.out blast.outfmt6 [transcripts.fasta]\n\n";
---- a/util/misc/nameSorted_SAM_to_FastQ.pl
-+++ b/util/misc/nameSorted_SAM_to_FastQ.pl
+--- trinityrnaseq.orig/util/misc/nameSorted_SAM_to_FastQ.pl
++++ trinityrnaseq/util/misc/nameSorted_SAM_to_FastQ.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -873,8 +883,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/nameSorted_SAM_to_paired_fastq.pl
-+++ b/util/misc/nameSorted_SAM_to_paired_fastq.pl
+--- trinityrnaseq.orig/util/misc/nameSorted_SAM_to_paired_fastq.pl
++++ trinityrnaseq/util/misc/nameSorted_SAM_to_paired_fastq.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -885,8 +895,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/pairwise_kmer_content_comparer.pl
-+++ b/util/misc/pairwise_kmer_content_comparer.pl
+--- trinityrnaseq.orig/util/misc/pairwise_kmer_content_comparer.pl
++++ trinityrnaseq/util/misc/pairwise_kmer_content_comparer.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -897,8 +907,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 file.fasta [kmer_length=25]\n\n";
---- a/util/misc/print_kmers.pl
-+++ b/util/misc/print_kmers.pl
+--- trinityrnaseq.orig/util/misc/print_kmers.pl
++++ trinityrnaseq/util/misc/print_kmers.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -909,8 +919,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 file.fa [kmer_length=25]\n\n";
---- a/util/misc/prop_pair_sam_refiner.pl
-+++ b/util/misc/prop_pair_sam_refiner.pl
+--- trinityrnaseq.orig/util/misc/prop_pair_sam_refiner.pl
++++ trinityrnaseq/util/misc/prop_pair_sam_refiner.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -921,8 +931,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/randomly_sample_PE_fastq.pl
-+++ b/util/misc/randomly_sample_PE_fastq.pl
+--- trinityrnaseq.orig/util/misc/randomly_sample_PE_fastq.pl
++++ trinityrnaseq/util/misc/randomly_sample_PE_fastq.pl
@@ -10,8 +10,7 @@
use strict;
use warnings;
@@ -933,8 +943,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
use File::Basename;
use List::Util qw(shuffle);
---- a/util/misc/run_HISAT.pl
-+++ b/util/misc/run_HISAT.pl
+--- trinityrnaseq.orig/util/misc/run_HISAT.pl
++++ trinityrnaseq/util/misc/run_HISAT.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -945,8 +955,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Pipeliner;
use File::Basename;
use Cwd;
---- a/util/misc/run_STAR.pl
-+++ b/util/misc/run_STAR.pl
+--- trinityrnaseq.orig/util/misc/run_STAR.pl
++++ trinityrnaseq/util/misc/run_STAR.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -957,8 +967,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Pipeliner;
use File::Basename;
use Cwd;
---- a/util/misc/run_STAR_via_samples_file.pl
-+++ b/util/misc/run_STAR_via_samples_file.pl
+--- trinityrnaseq.orig/util/misc/run_STAR_via_samples_file.pl
++++ trinityrnaseq/util/misc/run_STAR_via_samples_file.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -969,8 +979,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Pipeliner;
use File::Basename;
use Cwd;
---- a/util/misc/run_read_simulator_per_fasta_entry.pl
-+++ b/util/misc/run_read_simulator_per_fasta_entry.pl
+--- trinityrnaseq.orig/util/misc/run_read_simulator_per_fasta_entry.pl
++++ trinityrnaseq/util/misc/run_read_simulator_per_fasta_entry.pl
@@ -2,8 +2,7 @@
use strict;
@@ -981,7 +991,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
-@@ -41,7 +40,7 @@ main: {
+@@ -41,7 +40,7 @@
my $outfile = "$sim_out_dir/$outdir/$outdir.reads.fa";
@@ -990,9 +1000,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
if ($require_proper_pairs_flag) {
$cmd .= " --require_proper_pairs";
}
---- a/util/misc/simulate_illuminaPE_from_transcripts.pl
-+++ b/util/misc/simulate_illuminaPE_from_transcripts.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/util/misc/simulate_illuminaPE_from_transcripts.pl
++++ trinityrnaseq/util/misc/simulate_illuminaPE_from_transcripts.pl
+@@ -4,8 +4,7 @@
use warnings;
use Carp;
@@ -1002,9 +1012,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
---- a/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl
-+++ b/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl
++++ trinityrnaseq/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl
+@@ -4,8 +4,7 @@
use warnings;
use Carp;
@@ -1014,7 +1024,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
-@@ -118,9 +117,9 @@ main: {
+@@ -118,9 +117,9 @@
&process_cmd($cmd);
# convert to fasta format
@@ -1026,8 +1036,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
unlink("$left_prefix.fq", "$right_prefix.fq");
---- a/util/misc/sixFrameTranslation.pl
-+++ b/util/misc/sixFrameTranslation.pl
+--- trinityrnaseq.orig/util/misc/sixFrameTranslation.pl
++++ trinityrnaseq/util/misc/sixFrameTranslation.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1038,8 +1048,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Nuc_translator;
---- a/util/misc/sort_fastq.pl
-+++ b/util/misc/sort_fastq.pl
+--- trinityrnaseq.orig/util/misc/sort_fastq.pl
++++ trinityrnaseq/util/misc/sort_fastq.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1050,8 +1060,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
my $usage = "usage: $0 file.fastq\n\n";
---- a/util/misc/strip_fasta_header.pl
-+++ b/util/misc/strip_fasta_header.pl
+--- trinityrnaseq.orig/util/misc/strip_fasta_header.pl
++++ trinityrnaseq/util/misc/strip_fasta_header.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1062,9 +1072,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 file.fasta\n\n";
---- a/util/misc/transcript_coverage_UTR_trimmer.pl
-+++ b/util/misc/transcript_coverage_UTR_trimmer.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/transcript_coverage_UTR_trimmer.pl
++++ trinityrnaseq/util/misc/transcript_coverage_UTR_trimmer.pl
+@@ -5,9 +5,8 @@
use threads;
@@ -1075,7 +1085,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use WigParser;
use Fasta_reader;
use Statistics::Descriptive;
-@@ -71,7 +70,7 @@ if ($SS_lib_type && $SS_lib_type !~ /^(F
+@@ -71,7 +70,7 @@
die "Error, invalid --SS_lib_type, only F, R, FR, or RF are possible values";
}
@@ -1084,8 +1094,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
main: {
---- a/util/misc/transcript_fasta_to_ORF_pics.pl
-+++ b/util/misc/transcript_fasta_to_ORF_pics.pl
+--- trinityrnaseq.orig/util/misc/transcript_fasta_to_ORF_pics.pl
++++ trinityrnaseq/util/misc/transcript_fasta_to_ORF_pics.pl
@@ -1,7 +1,6 @@
#!/usr/bin/env perl
@@ -1095,8 +1105,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use strict;
use warnings;
---- a/util/misc/transcript_gff3_to_bed.pl
-+++ b/util/misc/transcript_gff3_to_bed.pl
+--- trinityrnaseq.orig/util/misc/transcript_gff3_to_bed.pl
++++ trinityrnaseq/util/misc/transcript_gff3_to_bed.pl
@@ -3,9 +3,7 @@
use strict;
use warnings;
@@ -1108,8 +1118,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
my $usage = "usage: $0 alignments.gff3\n\n";
---- a/util/misc/trinity_component_distribution.pl
-+++ b/util/misc/trinity_component_distribution.pl
+--- trinityrnaseq.orig/util/misc/trinity_component_distribution.pl
++++ trinityrnaseq/util/misc/trinity_component_distribution.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1120,8 +1130,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 Trinity.fasta [length_bin_size=100] [out_prefix='dist']\n\n";
---- a/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
-+++ b/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
++++ trinityrnaseq/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1132,8 +1142,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
-+++ b/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
++++ trinityrnaseq/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1144,8 +1154,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
-+++ b/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
++++ trinityrnaseq/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
@@ -1,8 +1,7 @@
#!/usr/bin/env perl
@@ -1156,8 +1166,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
-+++ b/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
++++ trinityrnaseq/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
@@ -1,8 +1,7 @@
#!/usr/bin/env perl
@@ -1168,8 +1178,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/SAM_filter_out_unmapped_reads.pl
-+++ b/util/support_scripts/SAM_filter_out_unmapped_reads.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_filter_out_unmapped_reads.pl
++++ trinityrnaseq/util/support_scripts/SAM_filter_out_unmapped_reads.pl
@@ -1,8 +1,7 @@
#!/usr/bin/env perl
@@ -1180,8 +1190,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/SAM_set_transcribed_orient_info.pl
-+++ b/util/support_scripts/SAM_set_transcribed_orient_info.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_set_transcribed_orient_info.pl
++++ trinityrnaseq/util/support_scripts/SAM_set_transcribed_orient_info.pl
@@ -1,8 +1,7 @@
#!/usr/bin/env perl
@@ -1192,8 +1202,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/SAM_strand_separator.pl
-+++ b/util/support_scripts/SAM_strand_separator.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_strand_separator.pl
++++ trinityrnaseq/util/support_scripts/SAM_strand_separator.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1204,8 +1214,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
use File::Basename;
---- a/util/support_scripts/SAM_to_frag_coords.pl
-+++ b/util/support_scripts/SAM_to_frag_coords.pl
+--- trinityrnaseq.orig/util/support_scripts/SAM_to_frag_coords.pl
++++ trinityrnaseq/util/support_scripts/SAM_to_frag_coords.pl
@@ -7,8 +7,7 @@
use strict;
use warnings;
@@ -1216,8 +1226,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/define_SAM_coverage_partitions2.pl
-+++ b/util/support_scripts/define_SAM_coverage_partitions2.pl
+--- trinityrnaseq.orig/util/support_scripts/define_SAM_coverage_partitions2.pl
++++ trinityrnaseq/util/support_scripts/define_SAM_coverage_partitions2.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1228,8 +1238,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use WigParser;
my $usage = "usage: $0 strand_coverage.wig strand[+-]\n\n";
---- a/util/support_scripts/define_coverage_partitions.pl
-+++ b/util/support_scripts/define_coverage_partitions.pl
+--- trinityrnaseq.orig/util/support_scripts/define_coverage_partitions.pl
++++ trinityrnaseq/util/support_scripts/define_coverage_partitions.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1240,9 +1250,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use WigParser;
my $usage = "usage: $0 strand_coverage.wig min_coverage strand[+-]\n\n";
---- a/util/support_scripts/extract_reads_per_partition.pl
-+++ b/util/support_scripts/extract_reads_per_partition.pl
-@@ -7,8 +7,7 @@ use Carp;
+--- trinityrnaseq.orig/util/support_scripts/extract_reads_per_partition.pl
++++ trinityrnaseq/util/support_scripts/extract_reads_per_partition.pl
+@@ -7,8 +7,7 @@
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
@@ -1252,8 +1262,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Nuc_translator;
use SAM_reader;
---- a/util/support_scripts/fastQ_to_fastA.pl
-+++ b/util/support_scripts/fastQ_to_fastA.pl
+--- trinityrnaseq.orig/util/support_scripts/fastQ_to_fastA.pl
++++ trinityrnaseq/util/support_scripts/fastQ_to_fastA.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1264,8 +1274,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Nuc_translator;
use IO::Uncompress::Gunzip;
---- a/util/support_scripts/fasta_to_tab.pl
-+++ b/util/support_scripts/fasta_to_tab.pl
+--- trinityrnaseq.orig/util/support_scripts/fasta_to_tab.pl
++++ trinityrnaseq/util/support_scripts/fasta_to_tab.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1276,8 +1286,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 [multiFastaFile] [NO_FULL_HEADER_FLAG=0]\n\n";
---- a/util/support_scripts/filter_iworm_by_min_length_or_cov.pl
-+++ b/util/support_scripts/filter_iworm_by_min_length_or_cov.pl
+--- trinityrnaseq.orig/util/support_scripts/filter_iworm_by_min_length_or_cov.pl
++++ trinityrnaseq/util/support_scripts/filter_iworm_by_min_length_or_cov.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1288,8 +1298,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/util/support_scripts/fragment_coverage_writer.pl
-+++ b/util/support_scripts/fragment_coverage_writer.pl
+--- trinityrnaseq.orig/util/support_scripts/fragment_coverage_writer.pl
++++ trinityrnaseq/util/support_scripts/fragment_coverage_writer.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1300,8 +1310,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/jaccard_fasta_clipper.pl
-+++ b/util/support_scripts/jaccard_fasta_clipper.pl
+--- trinityrnaseq.orig/util/support_scripts/jaccard_fasta_clipper.pl
++++ trinityrnaseq/util/support_scripts/jaccard_fasta_clipper.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1312,9 +1322,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 transcripts.fasta jaccard_clips.wig\n\n";
---- a/util/support_scripts/jaccard_wig_clipper.pl
-+++ b/util/support_scripts/jaccard_wig_clipper.pl
-@@ -6,8 +6,7 @@ use warnings;
+--- trinityrnaseq.orig/util/support_scripts/jaccard_wig_clipper.pl
++++ trinityrnaseq/util/support_scripts/jaccard_wig_clipper.pl
+@@ -6,8 +6,7 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
@@ -1324,8 +1334,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use WigParser;
---- a/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
-+++ b/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
+--- trinityrnaseq.orig/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
++++ trinityrnaseq/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1336,9 +1346,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/run_TMM_scale_matrix.pl
-+++ b/util/support_scripts/run_TMM_scale_matrix.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/util/support_scripts/run_TMM_scale_matrix.pl
++++ trinityrnaseq/util/support_scripts/run_TMM_scale_matrix.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
@@ -1349,7 +1359,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Data::Dumper;
my $usage = <<__EOUSAGE__;
-@@ -67,7 +66,6 @@ sub run_TMM {
+@@ -67,7 +66,6 @@
my $tmm_norm_script = "$counts_matrix_file.runTMM.R";
open (my $ofh, ">$tmm_norm_script") or die "Error, cannot write to $tmm_norm_script";
@@ -1357,9 +1367,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "library(edgeR)\n\n";
---- a/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
-+++ b/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
-@@ -5,9 +5,8 @@ use warnings;
+--- trinityrnaseq.orig/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
++++ trinityrnaseq/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
+@@ -5,9 +5,8 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
@@ -1370,7 +1380,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Data::Dumper;
-@@ -76,7 +75,6 @@ sub upper_quartile_normalize {
+@@ -76,7 +75,6 @@
my $tmm_norm_script = "__tmp_upper_quart_norm.R";
open (my $ofh, ">$tmm_norm_script") or die "Error, cannot write to $tmm_norm_script";
@@ -1378,8 +1388,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "data = read.table(\"$matrix_file\", header=T, row.names=1, com='')\n";
print $ofh "get_upper_quartile = function(vec) {\n"
---- a/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
-+++ b/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1390,7 +1400,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SingleLinkageClusterer;
use PSL_parser;
-@@ -302,7 +301,7 @@ sub examine_blat_mappings {
+@@ -302,7 +301,7 @@
my %mappings;
@@ -1399,8 +1409,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
open(my $fh, "$blat_output.stats") or die "Error, cannot open file $blat_output.stats";
---- a/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
-+++ b/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1411,8 +1421,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use PSL_parser;
use DelimParser;
---- a/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
-+++ b/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1423,9 +1433,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use PSL_parser;
require "overlapping_nucs.ph";
---- a/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
-+++ b/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
-@@ -7,8 +7,7 @@ use Carp;
+--- trinityrnaseq.orig/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
++++ trinityrnaseq/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
+@@ -7,8 +7,7 @@
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
@@ -1435,9 +1445,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Nuc_translator;
use SAM_reader;
---- a/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
-+++ b/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
-@@ -7,8 +7,7 @@ use Carp;
+--- trinityrnaseq.orig/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
++++ trinityrnaseq/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
+@@ -7,8 +7,7 @@
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
@@ -1447,8 +1457,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Nuc_translator;
use SAM_reader;
---- a/util/misc/blat_util/blat_sam_add_reads2.pl
-+++ b/util/misc/blat_util/blat_sam_add_reads2.pl
+--- trinityrnaseq.orig/util/misc/blat_util/blat_sam_add_reads2.pl
++++ trinityrnaseq/util/misc/blat_util/blat_sam_add_reads2.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1459,8 +1469,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Nuc_translator;
my $usage = "usage: $0 blat.psl.nameSorted.sam reads.tab.nameSorted\n\n";
---- a/util/misc/blat_util/process_BLAT_alignments.pl
-+++ b/util/misc/blat_util/process_BLAT_alignments.pl
+--- trinityrnaseq.orig/util/misc/blat_util/process_BLAT_alignments.pl
++++ trinityrnaseq/util/misc/blat_util/process_BLAT_alignments.pl
@@ -1,7 +1,6 @@
#!/usr/bin/env perl
@@ -1470,7 +1480,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use strict;
use warnings;
-@@ -66,7 +65,6 @@ my $genome_db = $opt_g;
+@@ -66,7 +65,6 @@
my $transcript_db = $opt_t;
my $output_prefix = $opt_o || "blat";
my $blat_path = "blat";
@@ -1478,7 +1488,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
unless ($genome_db && $transcript_db) {
die "$usage\n";
-@@ -171,7 +169,7 @@ my @top_hits_files;
+@@ -171,7 +169,7 @@
foreach my $pslx_file (@pslx_files) {
@@ -1487,7 +1497,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $completed_checkpoint_file = "$pslx_file.top_${num_top_hits}.completed";
unless (-e $completed_checkpoint_file) {
-@@ -220,7 +218,7 @@ foreach my $top_hits_file (@top_hits_fil
+@@ -220,7 +218,7 @@
# convert to gff3 format
print STDERR "-converting $top_hits_file to gff3\n";
@@ -1496,8 +1506,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
}
---- a/util/misc/blat_util/top_blat_sam_extractor.pl
-+++ b/util/misc/blat_util/top_blat_sam_extractor.pl
+--- trinityrnaseq.orig/util/misc/blat_util/top_blat_sam_extractor.pl
++++ trinityrnaseq/util/misc/blat_util/top_blat_sam_extractor.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1508,8 +1518,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
-+++ b/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
+--- trinityrnaseq.orig/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
++++ trinityrnaseq/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1520,8 +1530,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Gene_obj;
use GFF3_utils;
use BED_utils;
---- a/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
-+++ b/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1532,7 +1542,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use DelimParser;
use File::Basename;
use Data::Dumper;
-@@ -144,7 +143,7 @@ main: {
+@@ -144,7 +143,7 @@
}
@@ -1541,9 +1551,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
exit(0);
---- a/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
-+++ b/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
+@@ -5,8 +5,7 @@
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -1553,9 +1563,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Data::Dumper;
---- a/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
-+++ b/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
-@@ -6,8 +6,7 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
++++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
+@@ -6,8 +6,7 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
@@ -1565,8 +1575,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Gene_obj;
---- a/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
-+++ b/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
+--- trinityrnaseq.orig/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
++++ trinityrnaseq/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1577,7 +1587,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Process_cmd;
use File::Basename;
-@@ -15,10 +14,10 @@ my $collectl_dir = $ARGV[0] or die $usag
+@@ -15,10 +14,10 @@
main: {
@@ -1590,9 +1600,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
exit(0);
---- a/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
-+++ b/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
++++ trinityrnaseq/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
+@@ -4,8 +4,7 @@
use warnings;
use Carp;
use Data::Dumper;
@@ -1602,8 +1612,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SingleLinkageClusterer;
use Overlap_piler;
---- a/util/misc/align_reads_launch_igv.pl
-+++ b/util/misc/align_reads_launch_igv.pl
+--- trinityrnaseq.orig/util/misc/align_reads_launch_igv.pl
++++ trinityrnaseq/util/misc/align_reads_launch_igv.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1614,9 +1624,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Pipeliner;
use Cwd;
---- a/util/misc/collate_fqs.pl
-+++ b/util/misc/collate_fqs.pl
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/collate_fqs.pl
++++ trinityrnaseq/util/misc/collate_fqs.pl
+@@ -5,8 +5,7 @@
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -1626,8 +1636,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fastq_reader;
use Data::Dumper;
---- a/util/misc/determine_RF_strand_specificity.pl
-+++ b/util/misc/determine_RF_strand_specificity.pl
+--- trinityrnaseq.orig/util/misc/determine_RF_strand_specificity.pl
++++ trinityrnaseq/util/misc/determine_RF_strand_specificity.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1638,8 +1648,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/misc/examine_strand_specificity.pl
-+++ b/util/misc/examine_strand_specificity.pl
+--- trinityrnaseq.orig/util/misc/examine_strand_specificity.pl
++++ trinityrnaseq/util/misc/examine_strand_specificity.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1650,7 +1660,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
use Process_cmd;
-@@ -81,7 +80,7 @@ main: {
+@@ -81,7 +80,7 @@
## plot it.
@@ -1659,8 +1669,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
---- a/util/misc/fasta_seq_length.pl
-+++ b/util/misc/fasta_seq_length.pl
+--- trinityrnaseq.orig/util/misc/fasta_seq_length.pl
++++ trinityrnaseq/util/misc/fasta_seq_length.pl
@@ -2,9 +2,8 @@
use strict;
@@ -1672,9 +1682,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $usage = "usage: $0 fastaFile\n\n";
---- a/util/misc/filter_similar_seqs_expr_and_strand_aware.pl
-+++ b/util/misc/filter_similar_seqs_expr_and_strand_aware.pl
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/filter_similar_seqs_expr_and_strand_aware.pl
++++ trinityrnaseq/util/misc/filter_similar_seqs_expr_and_strand_aware.pl
+@@ -5,8 +5,7 @@
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Data::Dumper;
@@ -1684,8 +1694,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $help_flag;
---- a/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl
-+++ b/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl
+--- trinityrnaseq.orig/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl
++++ trinityrnaseq/util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1696,8 +1706,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Nuc_translator;
use Data::Dumper;
---- a/util/misc/get_GC_content_dist.pl
-+++ b/util/misc/get_GC_content_dist.pl
+--- trinityrnaseq.orig/util/misc/get_GC_content_dist.pl
++++ trinityrnaseq/util/misc/get_GC_content_dist.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1708,8 +1718,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Process_cmd;
---- a/util/misc/run_HISAT2_via_samples_file.pl
-+++ b/util/misc/run_HISAT2_via_samples_file.pl
+--- trinityrnaseq.orig/util/misc/run_HISAT2_via_samples_file.pl
++++ trinityrnaseq/util/misc/run_HISAT2_via_samples_file.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1720,8 +1730,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Process_cmd;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Pipeliner;
---- a/util/misc/run_bowtie2.pl
-+++ b/util/misc/run_bowtie2.pl
+--- trinityrnaseq.orig/util/misc/run_bowtie2.pl
++++ trinityrnaseq/util/misc/run_bowtie2.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1732,8 +1742,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Process_cmd;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Carp;
---- a/util/support_scripts/ensure_coord_sorted_sam.pl
-+++ b/util/support_scripts/ensure_coord_sorted_sam.pl
+--- trinityrnaseq.orig/util/support_scripts/ensure_coord_sorted_sam.pl
++++ trinityrnaseq/util/support_scripts/ensure_coord_sorted_sam.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1744,8 +1754,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_reader;
use SAM_entry;
---- a/util/support_scripts/fasta_find_duplicates.pl
-+++ b/util/support_scripts/fasta_find_duplicates.pl
+--- trinityrnaseq.orig/util/support_scripts/fasta_find_duplicates.pl
++++ trinityrnaseq/util/support_scripts/fasta_find_duplicates.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1756,8 +1766,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
---- a/util/support_scripts/filter_transcripts_require_min_cov.pl
-+++ b/util/support_scripts/filter_transcripts_require_min_cov.pl
+--- trinityrnaseq.orig/util/support_scripts/filter_transcripts_require_min_cov.pl
++++ trinityrnaseq/util/support_scripts/filter_transcripts_require_min_cov.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1768,9 +1778,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use DelimParser;
use Carp;
---- a/util/support_scripts/iworm_LR_to_scaff_pairs.pl
-+++ b/util/support_scripts/iworm_LR_to_scaff_pairs.pl
-@@ -8,8 +8,7 @@ use Carp;
+--- trinityrnaseq.orig/util/support_scripts/iworm_LR_to_scaff_pairs.pl
++++ trinityrnaseq/util/support_scripts/iworm_LR_to_scaff_pairs.pl
+@@ -8,8 +8,7 @@
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Data::Dumper;
@@ -1780,8 +1790,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $MIN_CONTAINMENT = 96;
---- a/util/support_scripts/nbkc_merge_left_right_stats.pl
-+++ b/util/support_scripts/nbkc_merge_left_right_stats.pl
+--- trinityrnaseq.orig/util/support_scripts/nbkc_merge_left_right_stats.pl
++++ trinityrnaseq/util/support_scripts/nbkc_merge_left_right_stats.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1792,8 +1802,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use DelimParser;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
---- a/util/support_scripts/nbkc_normalize.pl
-+++ b/util/support_scripts/nbkc_normalize.pl
+--- trinityrnaseq.orig/util/support_scripts/nbkc_normalize.pl
++++ trinityrnaseq/util/support_scripts/nbkc_normalize.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1804,8 +1814,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use DelimParser;
---- a/util/support_scripts/outfmt6_add_percent_match_length.pl
-+++ b/util/support_scripts/outfmt6_add_percent_match_length.pl
+--- trinityrnaseq.orig/util/support_scripts/outfmt6_add_percent_match_length.pl
++++ trinityrnaseq/util/support_scripts/outfmt6_add_percent_match_length.pl
@@ -2,8 +2,7 @@
use strict;
@@ -1816,9 +1826,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use List::Util qw(min max);
---- a/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
-+++ b/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
-@@ -7,9 +7,8 @@ use Carp;
+--- trinityrnaseq.orig/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
++++ trinityrnaseq/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
+@@ -7,9 +7,8 @@
use threads;
use File::Basename;
@@ -1829,7 +1839,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Thread_helper;
use Cwd;
-@@ -97,7 +96,7 @@ if ($SS_lib_type && $SS_lib_type !~ /^(F
+@@ -97,7 +96,7 @@
die "Error, invalid --SS_lib_type, only F, R, FR, or RF are possible values";
}
@@ -1838,8 +1848,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
main: {
---- a/util/support_scripts/salmon_runner.pl
-+++ b/util/support_scripts/salmon_runner.pl
+--- trinityrnaseq.orig/util/support_scripts/salmon_runner.pl
++++ trinityrnaseq/util/support_scripts/salmon_runner.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1850,8 +1860,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Process_cmd;
my $usage = "usage: $0 Trinity.fasta reads.fa\n\n";
---- a/util/support_scripts/scaffold_iworm_contigs.pl
-+++ b/util/support_scripts/scaffold_iworm_contigs.pl
+--- trinityrnaseq.orig/util/support_scripts/scaffold_iworm_contigs.pl
++++ trinityrnaseq/util/support_scripts/scaffold_iworm_contigs.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1862,9 +1872,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_entry;
my $usage = "\n\nusage: $0 nameSorted.sam iworm_fasta_file\n\n";
---- a/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
-+++ b/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
++++ trinityrnaseq/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
+@@ -4,8 +4,7 @@
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -1874,7 +1884,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Pipeliner;
use File::Basename;
-@@ -81,7 +80,7 @@ unless ($aligner =~ /^(STAR|HISAT2)$/i)
+@@ -81,7 +80,7 @@
$aligner = lc $aligner;
@@ -1883,7 +1893,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
main: {
-@@ -162,7 +161,7 @@ main: {
+@@ -162,7 +161,7 @@
$pipeliner->add_commands(new Command($cmd, "$analysis_token.$bam_file.fc.ok"));
@@ -1892,9 +1902,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
"$analysis_token.$bam_file.counts.ok"));
push (@counts_files, "$bam_file.counts");
---- a/Analysis/DifferentialExpression/diff_express.cgi
-+++ b/Analysis/DifferentialExpression/diff_express.cgi
-@@ -5,10 +5,9 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/diff_express.cgi
++++ trinityrnaseq/Analysis/DifferentialExpression/diff_express.cgi
+@@ -5,10 +5,9 @@
use CGI;
use CGI::Carp qw(fatalsToBrowser);
@@ -1906,8 +1916,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use CanvasXpress::Heatmap;
use BHStats;
---- a/util/TrinityStats.pl
-+++ b/util/TrinityStats.pl
+--- trinityrnaseq.orig/util/TrinityStats.pl
++++ trinityrnaseq/util/TrinityStats.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1918,8 +1928,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use BHStats;
---- a/util/analyze_blastPlus_topHit_coverage.pl
-+++ b/util/analyze_blastPlus_topHit_coverage.pl
+--- trinityrnaseq.orig/util/analyze_blastPlus_topHit_coverage.pl
++++ trinityrnaseq/util/analyze_blastPlus_topHit_coverage.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -1930,9 +1940,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
use Data::Dumper;
---- a/util/filter_low_expr_transcripts.pl
-+++ b/util/filter_low_expr_transcripts.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/util/filter_low_expr_transcripts.pl
++++ trinityrnaseq/util/filter_low_expr_transcripts.pl
+@@ -4,8 +4,7 @@
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -1942,9 +1952,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Fasta_reader;
my $help_flag;
---- a/util/insilico_read_normalization.pl
-+++ b/util/insilico_read_normalization.pl
-@@ -5,8 +5,7 @@ use warnings;
+--- trinityrnaseq.orig/util/insilico_read_normalization.pl
++++ trinityrnaseq/util/insilico_read_normalization.pl
+@@ -5,8 +5,7 @@
use threads;
no strict qw(subs refs);
@@ -1954,7 +1964,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Cwd;
use Carp;
-@@ -18,7 +17,7 @@ use Data::Dumper;
+@@ -18,7 +17,7 @@
use COMMON;
@@ -1963,7 +1973,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
open (STDERR, ">&STDOUT"); ## capturing stderr and stdout in a single stdout stream
-@@ -116,9 +115,9 @@ _EOUSAGE_
+@@ -116,9 +115,9 @@
;
@@ -1975,9 +1985,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
unless (@ARGV) {
die "$usage\n";
---- a/util/sift_bam_max_cov.pl
-+++ b/util/sift_bam_max_cov.pl
-@@ -4,8 +4,7 @@ use strict;
+--- trinityrnaseq.orig/util/sift_bam_max_cov.pl
++++ trinityrnaseq/util/sift_bam_max_cov.pl
+@@ -4,8 +4,7 @@
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -1987,9 +1997,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use SAM_entry;
my $help_flag;
---- a/Analysis/DifferentialExpression/PtR
-+++ b/Analysis/DifferentialExpression/PtR
-@@ -4,7 +4,6 @@ use strict;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/PtR
++++ trinityrnaseq/Analysis/DifferentialExpression/PtR
+@@ -4,7 +4,6 @@
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
@@ -1997,7 +2007,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
my $min_rowSums = 0;
-@@ -590,10 +589,10 @@ main: {
+@@ -590,10 +589,10 @@
# source these after potential data restoration above - in case they changed.
@@ -2012,9 +2022,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
$Rscript .= "data = primary_data\n";
---- a/Analysis/DifferentialExpression/analyze_diff_expr.pl
-+++ b/Analysis/DifferentialExpression/analyze_diff_expr.pl
-@@ -4,7 +4,6 @@ use strict;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/analyze_diff_expr.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/analyze_diff_expr.pl
+@@ -4,7 +4,6 @@
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
@@ -2022,7 +2032,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Data::Dumper;
my $usage = <<__EOUSAGE__;
-@@ -237,7 +236,7 @@ main: {
+@@ -237,7 +236,7 @@
sub cluster_diff_expressed_transcripts {
my ($diff_expr_matrix_file) = @_;
@@ -2031,7 +2041,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
if ($samples_file) {
$cmd .= " -s $samples_file";
-@@ -406,7 +405,7 @@ sub parse_result_files_find_diffExp {
+@@ -406,7 +405,7 @@
my $background_file = $result_file;
$background_file =~ s/\.DE_results$/\.count_matrix/ or die "Error, cannot modify $result_file to count_matrix name";
@@ -2040,7 +2050,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " --lengths $gene_lengths_file --genes_single_factor $condA_up_subset_file"
. " --background $background_file ";
-@@ -419,7 +418,7 @@ sub parse_result_files_find_diffExp {
+@@ -419,7 +418,7 @@
}
@@ -2049,7 +2059,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " --lengths $gene_lengths_file --genes_single_factor $condB_up_subset_file"
. " --background $background_file ";
-@@ -434,7 +433,7 @@ sub parse_result_files_find_diffExp {
+@@ -434,7 +433,7 @@
if ($countA + $countB) {
@@ -2058,7 +2068,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " --lengths $gene_lengths_file --genes_single_factor $either_subset_file"
. " --background $background_file ";
-@@ -447,7 +446,7 @@ sub parse_result_files_find_diffExp {
+@@ -447,7 +446,7 @@
}
if ($RUN_GOPLOT) {
@@ -2067,7 +2077,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " --DE_subset $either_subset_file "
. " --DE_GO_enriched $either_subset_file.GOseq.enriched "
. " --tmpdir $either_subset_file.GOseq.enriched.GOplot_dat"
-@@ -534,7 +533,7 @@ sub write_matrix_generate_heatmap {
+@@ -534,7 +533,7 @@
}
close $ofh;
@@ -2076,9 +2086,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
if ($samples_file) {
$cmd .= " -s $samples_file ";
---- a/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
-+++ b/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
-@@ -5,7 +5,6 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
+@@ -5,7 +5,6 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
@@ -2086,7 +2096,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = <<__EOUSAGE__;
-@@ -88,7 +87,7 @@ main: {
+@@ -88,7 +87,7 @@
#print $ofh "library(gplots)\n";
print $ofh "library(Biobase)\n";
print $ofh "library(fastcluster)\n";
@@ -2095,9 +2105,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "load(\"$R_data_file\")\n";
---- a/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
-+++ b/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
-@@ -5,7 +5,6 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
+@@ -5,7 +5,6 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
@@ -2105,7 +2115,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = <<__EOUSAGE__;
-@@ -89,7 +88,7 @@ main: {
+@@ -89,7 +88,7 @@
#print $ofh "library(gplots)\n";
print $ofh "library(Biobase)\n";
print $ofh "library(fastcluster)\n";
@@ -2114,7 +2124,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "load(\"$R_data_file\")\n";
-@@ -191,7 +190,7 @@ main: {
+@@ -191,7 +190,7 @@
chdir $outdir or die "Error, cannot cd into $outdir";
@@ -2123,9 +2133,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
---- a/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
-+++ b/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
-@@ -4,8 +4,6 @@ use strict;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
+@@ -4,8 +4,6 @@
use warnings;
use Carp;
@@ -2134,7 +2144,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
-@@ -101,7 +99,7 @@ main: {
+@@ -101,7 +99,7 @@
}
## generate a heatmap
@@ -2143,9 +2153,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
if ($samples_file) {
$cmd .= " -s $samples_file ";
}
---- a/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
-+++ b/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
-@@ -5,7 +5,6 @@ use warnings;
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
+@@ -5,7 +5,6 @@
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
@@ -2153,8 +2163,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Data::Dumper;
my $help_flag;
---- a/Analysis/DifferentialExpression/run_GOseq.pl
-+++ b/Analysis/DifferentialExpression/run_GOseq.pl
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/run_GOseq.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/run_GOseq.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2163,8 +2173,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
---- a/Analysis/DifferentialExpression/stratify_diff_expression.pl
-+++ b/Analysis/DifferentialExpression/stratify_diff_expression.pl
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/stratify_diff_expression.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/stratify_diff_expression.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2173,7 +2183,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "\n\nusage: $0 edgeR_dir\n\n";
-@@ -21,7 +20,7 @@ for my $fold_change (1..8) {
+@@ -21,7 +20,7 @@
for my $pvalue (2..10) {
@@ -2182,8 +2192,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
---- a/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
-+++ b/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
+--- trinityrnaseq.orig/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
++++ trinityrnaseq/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
@@ -3,8 +3,7 @@
use strict;
use warnings;
@@ -2194,8 +2204,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use CanvasXpress::Heatmap;
use CanvasXpress::PlotOnLoader;
use CanvasXpress::Line;
---- a/Analysis/FL_reconstruction_analysis/compute_oracle.pl
-+++ b/Analysis/FL_reconstruction_analysis/compute_oracle.pl
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/compute_oracle.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/compute_oracle.pl
@@ -3,8 +3,6 @@
use strict;
use warnings;
@@ -2205,7 +2215,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 reads.fasta ref_transcripts.fasta [SS]\n\n";
my $reads_file = $ARGV[0] or die $usage;
-@@ -12,7 +10,7 @@ my $ref_transcripts_fasta = $ARGV[1] or
+@@ -12,7 +10,7 @@
my $SS_flag = $ARGV[2] || 0;
@@ -2214,8 +2224,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " --reads $reads_file "
. " --checkFastaPath $ref_transcripts_fasta ";
---- a/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
-+++ b/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2224,8 +2234,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 file.paralog_clusters file.maps\n\n";
---- a/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
-+++ b/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
+--- trinityrnaseq.orig/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
++++ trinityrnaseq/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2234,7 +2244,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 genes.fasta transcripts.fasta max_intron BLAT_CPU [STRAND-SPECIFIC_FLAG=0]\n\n";
-@@ -16,14 +15,14 @@ my $SS = $ARGV[4] || 0;
+@@ -16,14 +15,14 @@
main: {
## run blat:
@@ -2251,8 +2261,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
exit(0);
---- a/util/abundance_estimates_to_matrix.pl
-+++ b/util/abundance_estimates_to_matrix.pl
+--- trinityrnaseq.orig/util/abundance_estimates_to_matrix.pl
++++ trinityrnaseq/util/abundance_estimates_to_matrix.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2261,7 +2271,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Carp;
-@@ -362,11 +361,11 @@ sub perform_cross_sample_norm {
+@@ -362,11 +361,11 @@
my ($tpm_matrix_file, $out_prefix_name) = @_;
if ($cross_sample_norm =~ /^TMM$/i) {
@@ -2275,9 +2285,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
}
elsif ($cross_sample_norm =~ /^none$/i) {
---- a/util/misc/TophatCufflinksWrapper.pl
-+++ b/util/misc/TophatCufflinksWrapper.pl
-@@ -6,7 +6,6 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/TophatCufflinksWrapper.pl
++++ trinityrnaseq/util/misc/TophatCufflinksWrapper.pl
+@@ -6,7 +6,6 @@
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
@@ -2285,8 +2295,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Cwd;
my $usage = <<__EOUSAGE__;
---- a/util/misc/bam_gene_tests/write_trin_cmds.pl
-+++ b/util/misc/bam_gene_tests/write_trin_cmds.pl
+--- trinityrnaseq.orig/util/misc/bam_gene_tests/write_trin_cmds.pl
++++ trinityrnaseq/util/misc/bam_gene_tests/write_trin_cmds.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2295,7 +2305,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
-@@ -70,7 +69,7 @@ while (<$fh>) {
+@@ -70,7 +69,7 @@
my $file = pop @x;
@@ -2304,8 +2314,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print "$cmd\n";
}
---- a/util/misc/blat_util/blat_to_sam.pl
-+++ b/util/misc/blat_util/blat_to_sam.pl
+--- trinityrnaseq.orig/util/misc/blat_util/blat_to_sam.pl
++++ trinityrnaseq/util/misc/blat_util/blat_to_sam.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2314,7 +2324,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Cwd;
use Getopt::Long qw(:config no_ignore_case bundling);
-@@ -72,9 +71,7 @@ unless ($genome_fa && $reads_fa) {
+@@ -72,9 +71,7 @@
main: {
@@ -2325,7 +2335,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd) unless (-s "$reads_fa.tab");
$cmd = "sort -T . -S 2G -k 1,1 $reads_fa.tab > $reads_fa.tab.sort";
-@@ -90,11 +87,11 @@ main: {
+@@ -90,11 +87,11 @@
# add the reads
@@ -2339,8 +2349,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
$cmd = "$FindBin::RealBin/cigar_tweaker $reads_fa.psl.sam.wReads.top $genome_fa > $reads_fa.psl.sam.wReads.top.tweaked";
---- a/util/misc/count_trans_per_component.pl
-+++ b/util/misc/count_trans_per_component.pl
+--- trinityrnaseq.orig/util/misc/count_trans_per_component.pl
++++ trinityrnaseq/util/misc/count_trans_per_component.pl
@@ -3,8 +3,6 @@
use strict;
use warnings;
@@ -2350,8 +2360,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 bfly.A.fasta [bfly.B.fasta ...]\n\n";
my @files = @ARGV or die $usage;
---- a/util/misc/frag_to_bed.pl
-+++ b/util/misc/frag_to_bed.pl
+--- trinityrnaseq.orig/util/misc/frag_to_bed.pl
++++ trinityrnaseq/util/misc/frag_to_bed.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2360,8 +2370,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use lib ("$ENV{EUK_MODULES}");
use Gene_obj;
---- a/util/misc/genome_gff3_to_gene_gff3_partitions.pl
-+++ b/util/misc/genome_gff3_to_gene_gff3_partitions.pl
+--- trinityrnaseq.orig/util/misc/genome_gff3_to_gene_gff3_partitions.pl
++++ trinityrnaseq/util/misc/genome_gff3_to_gene_gff3_partitions.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2370,8 +2380,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use lib ("$ENV{TRINITY_HOME}/PerlLib");
use Gene_obj;
use Fasta_reader;
---- a/util/misc/plot_expressed_gene_dist.pl
-+++ b/util/misc/plot_expressed_gene_dist.pl
+--- trinityrnaseq.orig/util/misc/plot_expressed_gene_dist.pl
++++ trinityrnaseq/util/misc/plot_expressed_gene_dist.pl
@@ -3,15 +3,13 @@
use strict;
use warnings;
@@ -2389,8 +2399,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print $ofh "pdf(\"$fpkm_file.genes_vs_minFPKM.pdf\")\n";
print $ofh "plot_expressed_gene_counts(\"$fpkm_file\", title=\"expressed transcripts vs. min FPKM\", fpkm_range=seq(0,5,0.01), outfile=\"$fpkm_file.genes_vs_minFPKM.dat\")\n";
print $ofh "dev.off()\n";
---- a/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
-+++ b/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
+--- trinityrnaseq.orig/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
++++ trinityrnaseq/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2399,8 +2409,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Cwd;
---- a/util/misc/run_GSNAP.pl
-+++ b/util/misc/run_GSNAP.pl
+--- trinityrnaseq.orig/util/misc/run_GSNAP.pl
++++ trinityrnaseq/util/misc/run_GSNAP.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2409,8 +2419,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Cwd;
---- a/util/misc/run_HiCpipe_bowtie.pl
-+++ b/util/misc/run_HiCpipe_bowtie.pl
+--- trinityrnaseq.orig/util/misc/run_HiCpipe_bowtie.pl
++++ trinityrnaseq/util/misc/run_HiCpipe_bowtie.pl
@@ -3,9 +3,6 @@
use strict;
use warnings;
@@ -2421,7 +2431,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 genome.fasta left.fq right.fq [output_dir]\n\n";
my $genome_file = $ARGV[0] or die $usage;
-@@ -26,7 +23,7 @@ main: {
+@@ -26,7 +23,7 @@
. " -- -a -m 1 --best --strata -p 4 --chunkmbs 512 ";
&process_cmd($cmd) unless (-s "$output_dir/$output_dir.nameSorted.sam");
@@ -2430,8 +2440,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd) unless (-s "$output_dir/$output_dir.raw");
---- a/util/misc/run_TOPHAT.pl
-+++ b/util/misc/run_TOPHAT.pl
+--- trinityrnaseq.orig/util/misc/run_TOPHAT.pl
++++ trinityrnaseq/util/misc/run_TOPHAT.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2440,8 +2450,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Cwd;
use Carp;
---- a/util/misc/run_bwa.pl
-+++ b/util/misc/run_bwa.pl
+--- trinityrnaseq.orig/util/misc/run_bwa.pl
++++ trinityrnaseq/util/misc/run_bwa.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2450,8 +2460,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Cwd;
use File::Basename;
use Carp;
---- a/util/misc/run_jellyfish.pl
-+++ b/util/misc/run_jellyfish.pl
+--- trinityrnaseq.orig/util/misc/run_jellyfish.pl
++++ trinityrnaseq/util/misc/run_jellyfish.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2460,9 +2470,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "\n\nusage: $0 reads.fa hash_size\n\n";
---- a/util/misc/run_read_simulator_per_gene.pl
-+++ b/util/misc/run_read_simulator_per_gene.pl
-@@ -5,8 +5,6 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/run_read_simulator_per_gene.pl
++++ trinityrnaseq/util/misc/run_read_simulator_per_gene.pl
+@@ -5,8 +5,6 @@
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
@@ -2471,7 +2481,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 file.fasta [max_genes]\n\n";
-@@ -69,7 +67,7 @@ main: {
+@@ -69,7 +67,7 @@
my $outfile = "$sim_out_dir/$outdir/$outdir.reads.fa";
@@ -2480,9 +2490,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
$gene_counter++;
---- a/util/misc/run_trimmomatic_qual_trimming.pl
-+++ b/util/misc/run_trimmomatic_qual_trimming.pl
-@@ -5,8 +5,6 @@ use warnings;
+--- trinityrnaseq.orig/util/misc/run_trimmomatic_qual_trimming.pl
++++ trinityrnaseq/util/misc/run_trimmomatic_qual_trimming.pl
+@@ -5,8 +5,6 @@
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
@@ -2491,7 +2501,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = <<__EOUSAGE__;
###############################################################
-@@ -72,7 +70,7 @@ main: {
+@@ -72,7 +70,7 @@
if ($left && $right) {
@@ -2500,7 +2510,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " $left $right "
. " $left.P.qtrim.fq $left.U.qtrim.fq "
. " $right.P.qtrim.fq $right.U.qtrim.fq "
-@@ -80,7 +78,7 @@ main: {
+@@ -80,7 +78,7 @@
}
else {
@@ -2509,8 +2519,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
. " $single "
. " $single.qtrim.fq "
. " $trim_params ";
---- a/util/misc/sim_test_framework/info_files_to_eval_cmds.pl
-+++ b/util/misc/sim_test_framework/info_files_to_eval_cmds.pl
+--- trinityrnaseq.orig/util/misc/sim_test_framework/info_files_to_eval_cmds.pl
++++ trinityrnaseq/util/misc/sim_test_framework/info_files_to_eval_cmds.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2519,7 +2529,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = "usage: $0 info_files.list.txt output_basedir [eval cmds]\n\n";
-@@ -19,7 +18,7 @@ main: {
+@@ -19,7 +18,7 @@
my @files = `cat $files_listing_file`;
chomp @files;
@@ -2528,8 +2538,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $basedir = cwd();
unless ($output_basedir =~ /^\//) {
---- a/util/misc/sim_test_framework/partition_target_transcripts.pl
-+++ b/util/misc/sim_test_framework/partition_target_transcripts.pl
+--- trinityrnaseq.orig/util/misc/sim_test_framework/partition_target_transcripts.pl
++++ trinityrnaseq/util/misc/sim_test_framework/partition_target_transcripts.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2538,8 +2548,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use lib ("$ENV{TRINITY_HOME}/PerlLib/");
use Fasta_reader;
use Cwd;
---- a/util/misc/sim_test_framework/run_Trinity_eval.pl
-+++ b/util/misc/sim_test_framework/run_Trinity_eval.pl
+--- trinityrnaseq.orig/util/misc/sim_test_framework/run_Trinity_eval.pl
++++ trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2548,7 +2558,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use lib ("$ENV{TRINITY_HOME}/PerlLib/");
use Fasta_reader;
use Cwd;
-@@ -142,7 +141,7 @@ unless ($ref_trans_fa && $BFLY_JAR && $l
+@@ -142,7 +141,7 @@
$NO_CLEANUP = 1; ## NEEDED NOW for iworm and bfy pruning assessment
unless ($ENV{TRINITY_HOME}) {
@@ -2557,7 +2567,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
}
my $reconstructions_log_file = "$OUT_DIR.reconstruction_summary.txt";
-@@ -203,7 +202,7 @@ main: {
+@@ -203,7 +202,7 @@
print $summary;
close $ofh;
@@ -2566,7 +2576,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
exit(0);
-@@ -423,7 +422,7 @@ sub check_inchworm_kmer_content {
+@@ -423,7 +422,7 @@
sub check_pruning {
my ($log_file, $ref_kmers_file) = @_;
@@ -2575,8 +2585,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
if ($pruned_ref_edges =~ /\w/) {
print "Pruned precious edges: $pruned_ref_edges\n";
---- a/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl
-+++ b/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl
+--- trinityrnaseq.orig/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl
++++ trinityrnaseq/util/misc/sim_test_framework/run_simulate_reads.wgsim.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2585,7 +2595,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use lib ("$ENV{TRINITY_HOME}/PerlLib/");
use Fasta_reader;
use Cwd;
-@@ -95,7 +94,7 @@ unless ($ref_trans_fa && $OUT_DIR) {
+@@ -95,7 +94,7 @@
unless ($ENV{TRINITY_HOME}) {
@@ -2594,8 +2604,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
}
---- a/util/misc/sim_test_framework/write_simulate_read_commands.pl
-+++ b/util/misc/sim_test_framework/write_simulate_read_commands.pl
+--- trinityrnaseq.orig/util/misc/sim_test_framework/write_simulate_read_commands.pl
++++ trinityrnaseq/util/misc/sim_test_framework/write_simulate_read_commands.pl
@@ -2,7 +2,6 @@
use strict;
@@ -2604,7 +2614,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
my $usage = "\n\n\tusage: $0 target_trans_files.list [opts ex. --wgsim ...]\n\n";
-@@ -18,7 +17,7 @@ main: {
+@@ -18,7 +17,7 @@
foreach my $file (@ref_files) {
my $outdir = dirname($file);
@@ -2613,8 +2623,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print "$cmd\n";
}
---- a/util/misc/simulate_reads_sam_and_fa.pl
-+++ b/util/misc/simulate_reads_sam_and_fa.pl
+--- trinityrnaseq.orig/util/misc/simulate_reads_sam_and_fa.pl
++++ trinityrnaseq/util/misc/simulate_reads_sam_and_fa.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2623,7 +2633,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use lib "$ENV{TRINITY_HOME}/PerlLib";
use Simulate::Uniform_Read_Generator;
use Overlap_info;
-@@ -353,7 +352,7 @@ main: {
+@@ -353,7 +352,7 @@
=strand_sep_trans
if ($SS_lib_type) {
@@ -2632,7 +2642,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
foreach my $sam_file ("$trans_sam_outfile.coordSorted.bam.+.sam", "$trans_sam_outfile.coordSorted.bam.-.sam") {
-@@ -398,7 +397,7 @@ main: {
+@@ -398,7 +397,7 @@
=strand_sep_genome
if ($SS_lib_type) {
@@ -2641,9 +2651,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
&process_cmd($cmd);
foreach my $sam_file ("$genome_sam_outfile.coordSorted.bam.+.sam", "$genome_sam_outfile.coordSorted.bam.-.sam") {
---- a/util/support_scripts/SAM_ordered_pair_jaccard.pl
-+++ b/util/support_scripts/SAM_ordered_pair_jaccard.pl
-@@ -4,7 +4,6 @@ use strict;
+--- trinityrnaseq.orig/util/support_scripts/SAM_ordered_pair_jaccard.pl
++++ trinityrnaseq/util/support_scripts/SAM_ordered_pair_jaccard.pl
+@@ -4,7 +4,6 @@
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
@@ -2651,7 +2661,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
-@@ -84,7 +83,7 @@ if (@ARGV) {
+@@ -84,7 +83,7 @@
}
@@ -2660,8 +2670,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
main: {
---- a/util/support_scripts/bowtie2_wrapper.pl
-+++ b/util/support_scripts/bowtie2_wrapper.pl
+--- trinityrnaseq.orig/util/support_scripts/bowtie2_wrapper.pl
++++ trinityrnaseq/util/support_scripts/bowtie2_wrapper.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2670,7 +2680,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Cwd;
use File::Basename;
use Carp;
-@@ -11,8 +10,6 @@ use Data::Dumper;
+@@ -11,8 +10,6 @@
use Getopt::Long qw(:config no_ignore_case bundling);
@@ -2679,7 +2689,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
$ENV{LC_ALL} = 'C'; # critical for proper sorting using [system "sort -k1,1 ..."] within the perl script
-@@ -171,7 +168,7 @@ if ($SS_lib_type && $SS_lib_type !~ /^(F
+@@ -171,7 +168,7 @@
}
@@ -2688,8 +2698,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my ($start_dir, $work_dir, $num_hits);
---- a/util/support_scripts/fastQ_to_tab.pl
-+++ b/util/support_scripts/fastQ_to_tab.pl
+--- trinityrnaseq.orig/util/support_scripts/fastQ_to_tab.pl
++++ trinityrnaseq/util/support_scripts/fastQ_to_tab.pl
@@ -3,8 +3,6 @@
use strict;
use warnings;
@@ -2699,9 +2709,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Getopt::Long qw(:config no_ignore_case bundling);
---- a/util/support_scripts/inchworm_transcript_splitter.pl
-+++ b/util/support_scripts/inchworm_transcript_splitter.pl
-@@ -5,13 +5,11 @@ use warnings;
+--- trinityrnaseq.orig/util/support_scripts/inchworm_transcript_splitter.pl
++++ trinityrnaseq/util/support_scripts/inchworm_transcript_splitter.pl
+@@ -5,13 +5,11 @@
use Getopt::Long qw(:config no_ignore_case bundling);
@@ -2716,8 +2726,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
my $usage = <<_EOUSAGE_;
---- a/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
-+++ b/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
+--- trinityrnaseq.orig/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
++++ trinityrnaseq/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2726,8 +2736,8 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use File::Basename;
use Cwd;
---- a/util/support_scripts/write_partitioned_trinity_cmds.pl
-+++ b/util/support_scripts/write_partitioned_trinity_cmds.pl
+--- trinityrnaseq.orig/util/support_scripts/write_partitioned_trinity_cmds.pl
++++ trinityrnaseq/util/support_scripts/write_partitioned_trinity_cmds.pl
@@ -3,7 +3,6 @@
use strict;
use warnings;
@@ -2736,7 +2746,7 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
-@@ -75,7 +74,7 @@ while (<$fh>) {
+@@ -75,7 +74,7 @@
my $file = pop @x;
@@ -2745,9 +2755,9 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
print "$cmd\n";
}
---- a/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
-+++ b/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
-@@ -143,7 +143,7 @@ def main():
+--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
++++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
+@@ -143,7 +143,7 @@
args = parser.parse_args()
@@ -2756,3 +2766,25 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
if not PICARD_HOME:
exit("Error, missing path to Picard-Tools in $PICARD_HOME.")
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
++++ trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
+@@ -20,7 +20,7 @@
+ ../../util/support_scripts/GG_write_trinity_cmds.pl --reads_list_file read_files.list --paired --SS > trinity_GG.cmds
+
+
+-../../trinity-plugins/parafly/bin/ParaFly -c trinity_GG.cmds -CPU 2 -vv
++/usr/bin/ParaFly -c trinity_GG.cmds -CPU 2 -vv
+
+ ## execute the trinity commands, and then pull together the aggregate fasta file like so:
+ find Dir_mm9chr17.tophat.* -name "*inity.fasta" | ../../util/GG_trinity_accession_incrementer.pl > mm9.Trinity-GG.fasta
+--- trinityrnaseq.orig/util/support_scripts/trinity_install_tests.sh
++++ trinityrnaseq/util/support_scripts/trinity_install_tests.sh
+@@ -41,7 +41,7 @@
+ fi
+
+
+-if [ -e "trinity-plugins/BIN/ParaFly" ]
++if [ -e "/usr/bin/ParaFly" ]
+ then
+ echo "parafly: has been Installed Properly"
+ else
=====================================
debian/patches/series
=====================================
@@ -19,3 +19,4 @@ skip_r-cran-argpase
skip_r-bioc-dexseq
skip_blat
fix-gcc-10.patch
+bamsifter_build
=====================================
debian/patches/update-paths
=====================================
@@ -3,9 +3,9 @@ Author: Michael R. Crusoe <mcrusoe at msu.edu>
Forwarded: no
Last-Updated: 2015-02-22
---- a/Trinity
-+++ b/Trinity
-@@ -369,7 +369,7 @@ my $full_usage = qq^
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -369,7 +369,7 @@
# --bfly_algorithm <string> : assembly algorithm to use. Options: @BFLY_ALGORITHMS
#
# --bfly_opts <string> :additional parameters to pass through to butterfly
@@ -14,9 +14,18 @@ Last-Updated: 2015-02-22
# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
#
#
---- a/Chrysalis/analysis/Chrysalis.cc
-+++ b/Chrysalis/analysis/Chrysalis.cc
-@@ -258,7 +258,7 @@ int main(int argc,char** argv)
+@@ -1014,7 +1014,7 @@
+ }
+
+ unless ($BFLY_JAR) {
+- $BFLY_JAR = "$BUTTERFLY_DIR/Butterfly.jar";
++ $BFLY_JAR = "/usr/share/java/Butterfly.jar";
+ }
+
+
+--- trinityrnaseq.orig/Chrysalis/analysis/Chrysalis.cc
++++ trinityrnaseq/Chrysalis/analysis/Chrysalis.cc
+@@ -258,7 +258,7 @@
commandArg<string> iwormStringCmmd("-iworm","inchworm file", "");
commandArg<string> oStringCmmd("-o","output directory");
commandArg<bool> pairsStringCmmd("-paired", "paired-end reads are used.", false);
@@ -25,8 +34,8 @@ Last-Updated: 2015-02-22
commandArg<bool> skipCmmd("-skip","skip initial 2 steps", false);
commandArg<bool> strandCmmd("-strand","strand-specific data", false);
commandArg<bool> nobreakCmmd("-nobreak","skip breaking", false);
---- a/trinity-plugins/bamsifter/Makefile
-+++ b/trinity-plugins/bamsifter/Makefile
+--- trinityrnaseq.orig/trinity-plugins/bamsifter/Makefile
++++ trinityrnaseq/trinity-plugins/bamsifter/Makefile
@@ -3,7 +3,7 @@
cwd = $(shell pwd)
@@ -36,3 +45,45 @@ Last-Updated: 2015-02-22
htslib/version.h :
+--- trinityrnaseq.orig/util/misc/bam_gene_tests/write_trin_cmds.pl
++++ trinityrnaseq/util/misc/bam_gene_tests/write_trin_cmds.pl
+@@ -23,7 +23,7 @@
+
+ # Example:
+ #
+-# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar ~/SVN/trinityrnaseq/trunk/Butterfly/Butterfly.jar --JM 1G --seqType fa
++# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar /usr/share/java/Butterfly.jar --JM 1G --seqType fa
+
+
+ __EOUSAGE__
+--- trinityrnaseq.orig/util/misc/compare_bflies.pl
++++ trinityrnaseq/util/misc/compare_bflies.pl
+@@ -37,7 +37,7 @@
+ my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
+ &process_cmd($cmd);
+
+- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/prev_vers/Butterfly_r2013_08_14.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
++ $cmd = "java -Xmx4G -jar $/usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
+
+ open (my $ofh, ">bfly.cmd") or die $!;
+ print $ofh $cmd;
+@@ -61,7 +61,7 @@
+ &process_cmd($cmd);
+
+
+- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
++ $cmd = "java -Xmx4G -jar /usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
+
+ open (my $ofh, ">bfly.cmd") or die $!;
+ print $ofh $cmd;
+--- trinityrnaseq.orig/util/misc/sim_test_framework/run_Trinity_eval.pl
++++ trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.pl
+@@ -17,7 +17,7 @@
+
+ my $help_flag;
+ my $ref_trans_fa;
+-my $BFLY_JAR = "$ENV{TRINITY_HOME}/Butterfly/Butterfly.jar";
++my $BFLY_JAR = "/usr/share/java/Butterfly.jar";
+ my $INCLUDE_REF_TRANS = 0;
+ my $OUT_DIR = "testing_dir";
+ my $MIN_CONTIG_LENGTH = 200;
=====================================
debian/trinityrnaseq.install
=====================================
@@ -8,7 +8,7 @@ trinity-plugins/seqtk-trinity/seqtk-trinity /usr/lib/trinityrnaseq/trinity-plugi
Trinity /usr/lib/trinityrnaseq
PerlLib /usr/lib/trinityrnaseq/
util /usr/lib/trinityrnaseq/
-trinity-plugins/bamsifter/bamsifter /usr/lib/trinityrnaseq/trinity-plugins/BIN/
+trinity-plugins/bamsifter/bamsifter /usr/lib/trinityrnaseq/trinity-plugins/bamsifter/
trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl /usr/lib/trinityrnaseq/trinity-plugins/COLLECTL/
trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py /usr/lib/trinityrnaseq/trinity-plugins/DEXseq_util/
PyLib/Pipeliner.py /usr/lib/trinityrnaseq/PyLib/
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/0d455157ba524208cb84b6d9b8d17a1756d6ce40...6c20b127f9edc81ce924ae43bd7782fb4d8e9412
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/0d455157ba524208cb84b6d9b8d17a1756d6ce40...6c20b127f9edc81ce924ae43bd7782fb4d8e9412
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