--- a/admin/Build_Trinotate_Boilerplate_SQLite_db.pl	2021-05-05 20:03:29.316610891 +0200
+++ b/admin/Build_Trinotate_Boilerplate_SQLite_db.pl	2021-05-05 20:27:51.503038659 +0200
@@ -14,10 +14,10 @@
 my $no_cleanup_flag = $ARGV[1] || 0;
 
 
-my $UTILDIR = "$FindBin::RealBin/util";
+my $UTILDIR = "$FindBin::RealBin";
 
 ## Resources:
-my $SPROT_DAT_URL = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz";
+my $SPROT_DAT_URL = "http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz";
 my $EGGNOG_DAT_URL = "http://eggnogdb.embl.de/download/eggnog_4.5/data/NOG/NOG.annotations.tsv.gz";
 my $GENE_ONTOLOGY_DAT_URL = "http://purl.obolibrary.org/obo/go/go-basic.obo";
 my $PFAM_DAT_URL = "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz";

--- a/sample_data/runMe.sh	2021-05-05 20:03:29.328610811 +0200
+++ b/sample_data/runMe.sh	2021-05-05 20:06:47.919310732 +0200
@@ -44,7 +44,7 @@
 echo Loading protein set
 echo "###############################"
 
-../Trinotate ${sqlite_db} init --gene_trans_map data/Trinity.fasta.gene_to_trans_map --transcript_fasta data/Trinity.fasta --transdecoder_pep data/Trinity.fasta.transdecoder.pep
+Trinotate ${sqlite_db} init --gene_trans_map data/Trinity.fasta.gene_to_trans_map --transcript_fasta data/Trinity.fasta --transdecoder_pep data/Trinity.fasta.transdecoder.pep
 
 
 
@@ -52,35 +52,35 @@
 echo Loading swissprot blast results
 echo "##############################"
 
-../Trinotate ${sqlite_db} LOAD_swissprot_blastp data/swissprot.blastp.outfmt6
-../Trinotate ${sqlite_db} LOAD_swissprot_blastx data/swissprot.blastx.outfmt6
+Trinotate ${sqlite_db} LOAD_swissprot_blastp data/swissprot.blastp.outfmt6
+Trinotate ${sqlite_db} LOAD_swissprot_blastx data/swissprot.blastx.outfmt6
 
 
 echo "#############################"
 echo Loading PFAM results
 echo "#############################"
 
-../Trinotate ${sqlite_db} LOAD_pfam data/TrinotatePFAM.out 
+Trinotate ${sqlite_db} LOAD_pfam data/TrinotatePFAM.out
 
 
 echo "############################"
 echo Loading TMHMM results
 echo "############################"
 
-../Trinotate ${sqlite_db} LOAD_tmhmm data/tmhmm.out
+Trinotate ${sqlite_db} LOAD_tmhmm data/tmhmm.out
 
 echo "###########################"
 echo Loading SignalP results
 echo "###########################"
 
-../Trinotate ${sqlite_db} LOAD_signalp data/signalp.out
+Trinotate ${sqlite_db} LOAD_signalp data/signalp.out
 
 
 #echo "###########################"
 #echo Loading RNAMMER results
 #echo "###########################"
 #
-#../Trinotate ${sqlite_db} LOAD_rnammer data/Trinity.fasta.rnammer.gff
+#Trinotate ${sqlite_db} LOAD_rnammer data/Trinity.fasta.rnammer.gff
 
 
 #################################################################
@@ -95,13 +95,13 @@
 echo "###################################################"
 
 # expression data load for genes
-../util/transcript_expression/import_expression_and_DE_results.pl --sqlite ${sqlite_db} --gene_mode \
+import_expression_and_DE_results.pl --sqlite ${sqlite_db} --gene_mode \
         --samples_file data/samples.txt \
         --count_matrix data/Trinity_genes.counts.matrix \
         --fpkm_matrix data/Trinity_genes.TMM.EXPR.matrix 
 
 # DE results load for genes
-../util/transcript_expression/import_expression_and_DE_results.pl --sqlite ${sqlite_db} --gene_mode \
+import_expression_and_DE_results.pl --sqlite ${sqlite_db} --gene_mode \
         --samples_file data/samples.txt \
         --DE_dir DESeq2_gene
 
@@ -111,13 +111,13 @@
 echo "##################################################"
 
 # expression data load for transcripts
-../util/transcript_expression/import_expression_and_DE_results.pl --sqlite ${sqlite_db} --transcript_mode \
+import_expression_and_DE_results.pl --sqlite ${sqlite_db} --transcript_mode \
         --samples_file data/samples.txt \
         --count_matrix data/Trinity_trans.counts.matrix \
         --fpkm_matrix data/Trinity_trans.TMM.EXPR.matrix
 
 # DE results load for transcripts
-../util/transcript_expression/import_expression_and_DE_results.pl --sqlite ${sqlite_db} --transcript_mode \
+import_expression_and_DE_results.pl --sqlite ${sqlite_db} --transcript_mode \
         --samples_file data/samples.txt \
         --DE_dir DESeq2_trans
 
@@ -128,29 +128,29 @@
 
 
 # import the transcription profile cluster stuff
-../util/transcript_expression/import_transcript_clusters.pl --group_name DE_all_vs_all --analysis_name diffExpr.P0.1_C1.matrix.RData.clusters_fixed_P_60 --sqlite ${sqlite_db} DESeq2_trans/diffExpr.P1e-3_C2.matrix.RData.clusters_fixed_P_60/*matrix
+import_transcript_clusters.pl --group_name DE_all_vs_all --analysis_name diffExpr.P0.1_C1.matrix.RData.clusters_fixed_P_60 --sqlite ${sqlite_db} DESeq2_trans/diffExpr.P1e-3_C2.matrix.RData.clusters_fixed_P_60/*matrix
 
 
 echo "###########################"
 echo Generating report table
 echo "###########################"
 
-../Trinotate ${sqlite_db} report > Trinotate_report.xls
+Trinotate ${sqlite_db} report > Trinotate_report.xls
 
 
 echo "#########################################"
 echo Extracting Gene Ontology Mappings Per Gene
 echo "#########################################"
 
-../util/extract_GO_assignments_from_Trinotate_xls.pl  --Trinotate_xls Trinotate_report.xls -G -I > Trinotate_report.xls.gene_ontology
+extract_GO_assignments_from_Trinotate_xls.pl  --Trinotate_xls Trinotate_report.xls -G -I > Trinotate_report.xls.gene_ontology
 
 # Load annotations
-../util/annotation_importer/import_transcript_names.pl ${sqlite_db} Trinotate_report.xls
+import_transcript_names.pl ${sqlite_db} Trinotate_report.xls
 
 
 
 # Generate trinotate report summary statistics
-../util/report_summary/trinotate_report_summary.pl Trinotate_report.xls Trinotate_report_stats
+trinotate_report_summary.pl Trinotate_report.xls Trinotate_report_stats
 
 
 echo "##########################"

--- a/Trinotate	2021-05-05 20:03:29.240611387 +0200
+++ b/Trinotate	2021-05-06 09:32:53.726437426 +0200
@@ -75,19 +75,19 @@
 
 my %command_to_params = ( 
                           # protein-based
-                          'LOAD_swissprot_blastp' => "$loaders_dir/Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastp --dbtype Swissprot",
-                          'LOAD_trembl_blastp' => "$loaders_dir/Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastp --dbtype TrEMBL",
-                          'LOAD_pfam'  => "$loaders_dir/Trinotate_PFAM_loader.pl --sqlite $sqlite_db --pfam $ARGV[0]",
-                          'LOAD_tmhmm' => "$loaders_dir/Trinotate_TMHMM_loader.pl --sqlite $sqlite_db --tmhmm $ARGV[0]",
-                          'LOAD_signalp' => "$loaders_dir/Trinotate_SIGNALP_loader.pl --sqlite $sqlite_db --signalp $ARGV[0]",
+                          'LOAD_swissprot_blastp' => "Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastp --dbtype Swissprot",
+                          'LOAD_trembl_blastp' => "Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastp --dbtype TrEMBL",
+                          'LOAD_pfam'  => "Trinotate_PFAM_loader.pl --sqlite $sqlite_db --pfam $ARGV[0]",
+                          'LOAD_tmhmm' => "Trinotate_TMHMM_loader.pl --sqlite $sqlite_db --tmhmm $ARGV[0]",
+                          'LOAD_signalp' => "Trinotate_SIGNALP_loader.pl --sqlite $sqlite_db --signalp $ARGV[0]",
                           
                           # transcript-based
-                          'LOAD_swissprot_blastx' => "$loaders_dir/Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastx --dbtype Swissprot",
-                          'LOAD_trembl_blastx' => "$loaders_dir/Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastx --dbtype TrEMBL",
-                          'LOAD_rnammer' => "$loaders_dir/Trinotate_RNAMMER_loader.pl --sqlite $sqlite_db --rnammer $ARGV[0]",
+                          'LOAD_swissprot_blastx' => "Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastx --dbtype Swissprot",
+                          'LOAD_trembl_blastx' => "Trinotate_BLAST_loader.pl --sqlite $sqlite_db --outfmt6 $ARGV[0] --prog blastx --dbtype TrEMBL",
+                          'LOAD_rnammer' => "Trinotate_RNAMMER_loader.pl --sqlite $sqlite_db --rnammer $ARGV[0]",
                           
                           # custom blast searches
-                          'LOAD_custom_blast' => "$loaders_dir/Trinotate_BLAST_loader.pl --sqlite $sqlite_db @ARGV",
+                          'LOAD_custom_blast' => "Trinotate_BLAST_loader.pl --sqlite $sqlite_db @ARGV",
     
     
     );
@@ -99,13 +99,13 @@
 }
 elsif ($command eq "report") {
     ## generate Trinotate report.
-    my $cmd = "$FindBin::RealBin/util/Trinotate_report_writer.pl --sqlite $sqlite_db @ARGV";
+    my $cmd = "Trinotate_report_writer.pl --sqlite $sqlite_db @ARGV";
     &process_cmd($cmd);
     
 }
 elsif ($command eq "init") {
     # populate sequence and gene/trans/orf data
-    my $cmd = "$FindBin::RealBin/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite $sqlite_db @ARGV --bulk_load";
+    my $cmd = "TrinotateSeqLoader.pl --sqlite $sqlite_db @ARGV --bulk_load";
     &process_cmd($cmd);
 }
 else {

--- a/util/report_summary/trinotate_report_summary.pl	2021-05-05 20:03:29.336610759 +0200
+++ b/util/report_summary/trinotate_report_summary.pl	2021-05-05 20:11:48.241344670 +0200
@@ -17,7 +17,7 @@
 my $TOP_TAX_LEVEL = 6;
 
 
-my $UTILDIR = "$FindBin::Bin/util";
+my $UTILDIR = "$FindBin::Bin";
 
 main: {
 
