[med-svn] [Git][med-team/trinityrnaseq][upstream] New upstream version 2.15.2+dfsg
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Aug 21 23:04:45 BST 2024
Michael R. Crusoe pushed to branch upstream at Debian Med / trinityrnaseq
Commits:
ae0404ed by Michael R. Crusoe at 2024-08-21T16:47:23+02:00
New upstream version 2.15.2+dfsg
- - - - -
30 changed files:
- Analysis/DifferentialExpression/PtR
- Analysis/DifferentialExpression/R/heatmap.3.R
- + Analysis/DifferentialExpression/dexseq_given_bams.pl
- Analysis/DifferentialExpression/run_GOseq.pl
- + Analysis/DifferentialExpression/sum_tech_replicates.pl
- Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
- Changelog.txt
- Docker/Dockerfile
- Docker/README.md
- README.md
- Trinity
- trinity-plugins/ParaFly/Makefile
- trinity-plugins/ParaFly/bin/ParaFly
- trinity-plugins/ParaFly/config.log
- trinity-plugins/ParaFly/config.status
- trinity-plugins/ParaFly/src/.deps/ParaFly.Po
- trinity-plugins/ParaFly/src/.deps/argProcessor.Po
- trinity-plugins/ParaFly/src/Makefile
- trinity-plugins/bamsifter/.gitmodules
- trinity-plugins/bamsifter/build_htslib.sh
- − trinity-plugins/bamsifter/htslib-1.16.tar.bz2
- trinity-plugins/bamsifter/sift_bam_max_cov.cpp
- util/align_and_estimate_abundance.pl
- util/insilico_read_normalization.pl
- util/misc/fastq_stats.pl
- util/misc/plot_ExN50_statistic.Rscript
- util/misc/process_minimap2_alignments.pl
- util/misc/run_STAR_via_samples_file.pl
- util/misc/try_estimate_TPM_filtering_threshold.Rscript
- + util/support_scripts/run_UpperQuartileNormalization_matrix.Rscript
Changes:
=====================================
Analysis/DifferentialExpression/PtR
=====================================
@@ -336,6 +336,9 @@ my $top_variable_via_stdev_and_mean_expr_flag = 0;
my $min_stdev_expr = undef;
my $min_mean_expr = undef;
+my $cexCol = 0.5;
+my $cexRow = 0.5;
+
my $imgfmt = "pdf"; # alt is svg
&GetOptions (
@@ -458,6 +461,9 @@ my $imgfmt = "pdf"; # alt is svg
## Misc params
'help|h' => \$help_flag,
'write_intermediate_data_tables' => \$write_intermediate_data_tables_flag,
+
+ 'cexRow=f' => \$cexRow,
+ 'cexCol=f' => \$cexCol,
'show_pipeline_flowchart' => \$show_pipeline_flowchart,
@@ -1077,7 +1083,7 @@ main: {
$Rscript .= "if (is.null(hc_samples)) { RowV=NULL; ColV=NULL} else { RowV=as.dendrogram(hc_samples); ColV=RowV }\n";
- $Rscript .= "heatmap.3(sample_cor_for_plot, dendrogram='both', Rowv=RowV, Colv=ColV, col = myheatcol, scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, symbreaks=F, margins=c(10,10), cexCol=1, cexRow=1, cex.main=0.75, main=paste(\"sample correlation matrix\n\", \"$output_prefix\") ";
+ $Rscript .= "heatmap.3(sample_cor_for_plot, dendrogram='both', Rowv=RowV, Colv=ColV, col = myheatcol, scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, symbreaks=F, margins=c(10,10), cexCol=$cexCol, cexRow=$cexRow, cex.main=0.75, main=paste(\"sample correlation matrix\n\", \"$output_prefix\") ";
if ($samples_file || $use_columns_as_samples || $sample_cor_sum_gene_factor_expr) {
@@ -1143,7 +1149,7 @@ main: {
$Rscript .= "sampleAnnotations_row_subset = sampleAnnotations[rownames(sampleAnnotations) \%in% subset_rowsamples, subset_rownames]\n";
- $Rscript .= "heatmap.3(sample_subset_cor_matrix, dendrogram='both', Rowv=as.dendrogram(hc_subset_row), Colv=as.dendrogram(hc_subset_col), col = greenred(75), scale='none', key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=1, cexRow=1, cex.main=0.75, main=paste(\"sample correlation matrix\n\", \"$output_prefix\"), ColSideColors=sampleAnnotations_col_subset, RowSideColors=t(sampleAnnotations_row_subset) ";
+ $Rscript .= "heatmap.3(sample_subset_cor_matrix, dendrogram='both', Rowv=as.dendrogram(hc_subset_row), Colv=as.dendrogram(hc_subset_col), col = greenred(75), scale='none', key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=$cexCol, cexRow=$cexRow, cex.main=0.75, main=paste(\"sample correlation matrix\n\", \"$output_prefix\"), ColSideColors=sampleAnnotations_col_subset, RowSideColors=t(sampleAnnotations_row_subset) ";
#$Rscript .= "heatmap.3(sample_cor, dendrogram='both', Rowv=as.dendrogram(hc_samples), Colv=as.dendrogram(hc_samples), col = greenred(75), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=1, cexRow=1, cex.main=0.75, main=paste(\"sample correlation matrix\n\", \"$output_prefix\") ";
#if ($samples_file || $use_columns_as_samples) {
@@ -1341,7 +1347,7 @@ main: {
}
- $Rscript .= "heatmap.3(gene_cor, dendrogram='both', Rowv=as.dendrogram(hc_genes), Colv=as.dendrogram(hc_genes), col=colorpanel(256,'purple','black','yellow'), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=1, cexRow=1, cex.main=0.75, main=paste(\"feature correlation matrix\n\", \"$output_prefix\" ) ";
+ $Rscript .= "heatmap.3(gene_cor, dendrogram='both', Rowv=as.dendrogram(hc_genes), Colv=as.dendrogram(hc_genes), col=colorpanel(256,'purple','black','yellow'), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=$cexCol, cexRow=$cexRow, cex.main=0.75, main=paste(\"feature correlation matrix\n\", \"$output_prefix\" ) ";
if ($gene_factors_file) {
$Rscript .= ", RowSideColors=geneFactorAnnotations, ColSideColors=t(geneFactorAnnotations)";
@@ -1504,7 +1510,7 @@ main: {
$Rowv = "F";
}
- $Rscript .= "heatmap.3(heatmap_data, dendrogram=\'$dendrogram\', Rowv=$Rowv, Colv=$Colv, col=myheatcol, scale=\"none\", density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=1, margins=c(10,10), cex.main=0.75, main=paste(\"samples vs. features\n\", \"$output_prefix\" ) ";
+ $Rscript .= "heatmap.3(heatmap_data, dendrogram=\'$dendrogram\', Rowv=$Rowv, Colv=$Colv, col=myheatcol, scale=\"none\", density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=$cexCol, margins=c(10,10), cex.main=0.75, main=paste(\"samples vs. features\n\", \"$output_prefix\" ) ";
if ($gene_factors_file) {
@@ -1607,7 +1613,7 @@ main: {
}
$Rscript .= "$imgfmt(\"$output_prefix.${var_method}_vs_count_hist.$imgfmt\")\n";
- $Rscript .= "heatmap.3(count_hist_matrix, Rowv=F, Colv=F, dendrogram='none', col=colorpanel(max(count_hist_matrix), low='black', high='yellow'), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=1, cexRow=1, cex.main=0.75, main=\"$var_method vs. count hist\", RowSideColors=t(cv_colors))\n";
+ $Rscript .= "heatmap.3(count_hist_matrix, Rowv=F, Colv=F, dendrogram='none', col=colorpanel(max(count_hist_matrix), low='black', high='yellow'), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=$cexCol, cexRow=$cexRow, cex.main=0.75, main=\"$var_method vs. count hist\", RowSideColors=t(cv_colors))\n";
$Rscript .= "dev.off()\n";
}
@@ -1740,7 +1746,7 @@ sub add_sample_QC_analysis_R {
. " samples_want = colnames(data) \%in% samples_want\n"
#. " print(samples_want)\n"
- . " if (sum(samples_want) > 1) {\n"
+ . " if (sum(samples_want) >= 1) {\n" # not sure why this was prev set to >1
. " $imgfmt(file=paste(sample_name, \'.rep_compare.$imgfmt\', sep='')";
if ($img_width) {
$Rscript .= ", width=$img_width";
@@ -1766,7 +1772,7 @@ sub add_sample_QC_analysis_R {
# . " pairs3(d, XY_convert_fun=function(x,y) qqplot(x,y,plot.it=F), main=paste('Replicate QQplots:', sample_name)) # QQ plots\n"
. " reps_cor = cor(d, method=\"$sample_cor\", use='pairwise.complete.obs')\n"
. " hc_samples = hclust(as.dist(1-reps_cor), method=\"complete\")\n"
- . " heatmap.3(reps_cor, dendrogram='both', Rowv=as.dendrogram(hc_samples), Colv=as.dendrogram(hc_samples), col = cm.colors(256), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symbreaks=F, margins=c(10,10), cexCol=1, cexRow=1, main=paste('Replicate Correlations:', sample_name) )\n"
+ . " heatmap.3(reps_cor, dendrogram='both', Rowv=as.dendrogram(hc_samples), Colv=as.dendrogram(hc_samples), col = cm.colors(256), scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symbreaks=F, margins=c(10,10), cexCol=$cexCol, cexRow=$cexRow, main=paste('Replicate Correlations:', sample_name) )\n"
. " dev.off()\n"
. " }\n"
. "}\n";
@@ -1927,7 +1933,7 @@ sub add_prin_comp_heatmaps {
$Rscript .= " write.table(selected_genes_matrix, file=paste(\"$output_prefix\", '.PC',i,'_extreme',$num_top_genes_PC_extreme,'.matrix', sep=''), quote=F, sep=\"\t\")\n";
- $Rscript .= " heatmap.3(selected_genes_matrix, col=myheatcol, scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=1, margins=c(10,10), cex.main=0.75, RowSideColors=pc_color_bar, cexRow=0.5, main=paste('heatmap for', $num_top_genes_PC_extreme, ' extreme of PC', i)";
+ $Rscript .= " heatmap.3(selected_genes_matrix, col=myheatcol, scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=$cexCol, margins=c(10,10), cex.main=0.75, RowSideColors=pc_color_bar, cexRow=$cexRow, main=paste('heatmap for', $num_top_genes_PC_extreme, ' extreme of PC', i)";
if ($samples_file) {
$Rscript .= ", ColSideColors=sampleAnnotations";
@@ -1942,7 +1948,7 @@ sub add_prin_comp_heatmaps {
$Rscript .= "write.table(all_selected_genes_matrix, file=paste(\"$output_prefix\", '.PC_all','_extreme',$num_top_genes_PC_extreme,'.matrix', sep=''), quote=F, sep=\"\t\")\n";
- $Rscript .= "heatmap.3(all_selected_genes_matrix, col=myheatcol, scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=1, margins=c(10,10), cex.main=0.75, cexRow=0.5, main=paste('heatmap for ALL selected ', $num_top_genes_PC_extreme, ' extreme of all PCs')";
+ $Rscript .= "heatmap.3(all_selected_genes_matrix, col=myheatcol, scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=0.5, margins=c(10,10), cex.main=0.75, cexRow=$cexRow, main=paste('heatmap for ALL selected ', $num_top_genes_PC_extreme, ' extreme of all PCs')";
if ($samples_file) {
$Rscript .= ", ColSideColors=sampleAnnotations";
@@ -1990,7 +1996,7 @@ sub add_top_loadings_pc_heatmap {
}
- $Rscript .= " heatmap.3(top_loadings_pc_matrix, col=myheatcol, scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=1, margins=c(10,10), cex.main=0.75, cexRow=0.5, main=paste('heatmap for', $top_loadings_pc_heatmap, ' extreme all Prin. Comps.')";
+ $Rscript .= " heatmap.3(top_loadings_pc_matrix, col=myheatcol, scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=$cexCol, margins=c(10,10), cex.main=0.75, cexRow=$cexRow, main=paste('heatmap for', $top_loadings_pc_heatmap, ' extreme all Prin. Comps.')";
if ($samples_file) {
$Rscript .= ", ColSideColors=sampleAnnotations";
@@ -2049,14 +2055,14 @@ sub write_study_individual_gene_correlations_function {
$Rscript .= " this_sample_cor = cor(gene_expr_submatrix, method=\"$sample_cor\", use='pairwise.complete.obs')\n"
. " this_hc_samples = hclust(as.dist(1-this_sample_cor), method=\"$sample_clust\")\n";
- $Rscript .= " heatmap.3(this_gene_cor_matrix, dendrogram='both', Rowv=as.dendrogram(this_hc_genes), Colv=as.dendrogram(this_hc_genes), col=myheatcol, scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=1, cexRow=1, cex.main=0.75, main=paste(\"feature correlation matrix\n\", gene_id))\n";
+ $Rscript .= " heatmap.3(this_gene_cor_matrix, dendrogram='both', Rowv=as.dendrogram(this_hc_genes), Colv=as.dendrogram(this_hc_genes), col=myheatcol, scale='none', symm=TRUE, key=TRUE,density.info='none', trace='none', symkey=FALSE, margins=c(10,10), cexCol=$cexCol, cexRow=$cexRow, cex.main=0.75, main=paste(\"feature correlation matrix\n\", gene_id))\n";
# gene vs. samples plot
# center rows
$Rscript .= " gene_expr_submatrix = t(scale(t(gene_expr_submatrix), scale=F))\n";
- $Rscript .= " heatmap.3(gene_expr_submatrix, col=myheatcol, Rowv=as.dendrogram(this_hc_genes), Colv=as.dendrogram(this_hc_samples), scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=1, margins=c(10,10), cex.main=0.75, cexRow=0.5, main=paste('heatmap for most correlated to', gene_id)";
+ $Rscript .= " heatmap.3(gene_expr_submatrix, col=myheatcol, Rowv=as.dendrogram(this_hc_genes), Colv=as.dendrogram(this_hc_samples), scale='none', density.info=\"none\", trace=\"none\", key=TRUE, keysize=1.2, cexCol=$cexCol, margins=c(10,10), cex.main=0.75, cexRow=$cexRow, main=paste('heatmap for most correlated to', gene_id)";
if ($samples_file) {
$Rscript .= ", ColSideColors=these_sample_annotations";
=====================================
Analysis/DifferentialExpression/R/heatmap.3.R
=====================================
@@ -99,12 +99,12 @@ heatmap.3 <- function(x,
warning("Using scale=\"row\" or scale=\"column\" when breaks are",
"specified can produce unpredictable results.", "Please consider using only one or the other.")
- if (is.null(Rowv) || is.na(Rowv))
+ if (all(is.null(Rowv)) || all(is.na(Rowv)))
Rowv <- FALSE
- if (is.null(Colv) || is.na(Colv))
+ if (all(is.null(Colv)) || all(is.na(Colv)))
Colv <- FALSE
- else if (Colv == "Rowv" && !isTRUE(Rowv))
+ else if (all(Colv == "Rowv") && !all(isTRUE(Rowv)))
Colv <- FALSE
if (length(di <- dim(x)) != 2 || !is.numeric(x))
=====================================
Analysis/DifferentialExpression/dexseq_given_bams.pl
=====================================
@@ -0,0 +1,246 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Carp;
+use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
+use FindBin;
+use lib "$FindBin::Bin/../../PerlLib";
+use Pipeliner;
+use File::Basename;
+
+my $CPU = 2;
+
+my $top_genes_plot = 50;
+
+my $usage = <<__EOUSAGE__;
+
+#################################################################
+#
+# Required:
+#
+# --genes_gtf <string> Trinity genes gtf file
+#
+# --samples_file <string> samples file for dexseq. Formatting is:
+# condition(tab)replicate_name(tab)/path/to/STAR/filename.bam
+#
+#
+# Optional:
+#
+# --out_prefix <string> default: 'dexseq'
+#
+# --CPU <int> default: $CPU
+#
+# --top_genes_plot <int> default: $top_genes_plot
+#
+# --SS_lib_type <string> strand-specific sequencing type {RF, FR, R, F}
+#
+# --unpaired indicate reads are unpaired.
+#
+################################################################
+
+
+__EOUSAGE__
+
+ ;
+
+# --aligner <string> hisat2|gsnap|STAR
+
+
+my $help_flag;
+my $genes_gtf_file;
+my $samples_file;
+my $out_prefix = "dexseq";
+my $aligner;
+my $SS_lib_type = "";
+my $genomeSAindexNbases;
+my $unpaired_reads_flag;
+
+
+&GetOptions ( 'h' => \$help_flag,
+ 'genes_gtf=s' => \$genes_gtf_file,
+ 'samples_file=s' => \$samples_file,
+ 'out_prefix=s' => \$out_prefix,
+ 'CPU=i' => \$CPU,
+ 'top_genes_plot=i' => \$top_genes_plot,
+ 'unpaired_reads' => \$unpaired_reads_flag,
+ 'SS_lib_type=s' => \$SS_lib_type,
+ );
+
+
+if ($help_flag) {
+ die $usage;
+}
+
+unless ($genes_gtf_file && $samples_file) {
+ die $usage;
+}
+
+my $TRINITY_HOME = "$FindBin::Bin/../..";
+
+main: {
+
+ my @samples_info = &parse_samples_file($samples_file);
+
+ my $pipeliner = new Pipeliner(-verbose => 2);
+
+
+ my $chkpts_dir = "dexseqG_chkpts";
+ unless(-d $chkpts_dir) {
+ mkdir $chkpts_dir or die "Error, cannot mkdir $chkpts_dir";
+ }
+
+ my $analysis_token = "$chkpts_dir/" . basename($genes_gtf_file);
+
+ ## flatten the gtf file
+ my $cmd = "$TRINITY_HOME/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py $genes_gtf_file $genes_gtf_file.dexseq.gff";
+ $pipeliner->add_commands(new Command($cmd, "$chkpts_dir/" . basename($genes_gtf_file) . ".flatten_gtf.ok"));
+
+
+ my @counts_files;
+ ## process each of the replicates
+ foreach my $sample_info_aref (@samples_info) {
+ my ($condition, $replicate, $bam_file) = @$sample_info_aref;
+
+ unless (-s $bam_file) {
+ die "Error, cannot locate bam file: $bam_file";
+ }
+
+ # quant
+ my $cmd = "featureCounts -T $CPU ";
+
+ # paired or unpaired:
+ unless ($unpaired_reads_flag) {
+ $cmd .= " -p -B ";
+ }
+
+ ## strand-specific options:
+ if ($SS_lib_type) {
+ if ($SS_lib_type =~ /^F/) {
+ $cmd .= " -s 1";
+ }
+ elsif ($SS_lib_type =~ /^R/) {
+ $cmd .= " -s 2";
+ }
+ else {
+ die "Error, not recognizing strand-specific lib type [$SS_lib_type]";
+ }
+ }
+ else {
+ # unstranded by default
+ }
+
+ $cmd .= " -O --fraction -M -t exonic_part -g exonic_gene_part_number -a $genes_gtf_file.dexseq.gff -f -o $bam_file.fc $bam_file";
+
+ $pipeliner->add_commands(new Command($cmd, "$analysis_token." . basename($bam_file) . ".fc.ok"));
+
+
+ $pipeliner->add_commands(new Command("$FindBin::Bin/../SuperTranscripts/DTU/util/reformat_featureCounts.pl $bam_file.fc > $bam_file.counts",
+ "$analysis_token." . basename($bam_file) . ".counts.ok"));
+
+ push (@counts_files, "$bam_file.counts");
+
+ }
+
+ #############
+ ## run DEXseq
+
+ # first write a samples table
+ my $samples_table_file = "$out_prefix.sample_table";
+ {
+ open (my $ofh, ">$samples_table_file") or die "Error, cannot write to $samples_table_file";
+
+ print $ofh "\t" . join("\t", "condition", "counts_filename") . "\n";
+ for (my $i = 0; $i <= $#samples_info; $i++) {
+ my $sample_info_aref = $samples_info[$i];
+ my ($condition, $replicate_name, $left_fq, $right_fq) = @$sample_info_aref;
+ my $counts_file = $counts_files[$i];
+
+ print $ofh join("\t", $replicate_name, $condition, $counts_file) . "\n";
+ }
+
+ close $ofh;
+ }
+
+ my $dexseq_rscript = "$out_prefix.dexseq.Rscript";
+ if ($out_prefix !~ /dexseq/i) {
+ $out_prefix .= ".dexseq";
+ }
+
+ {
+
+ open (my $ofh, ">$dexseq_rscript") or die "Error, cannot write to $dexseq_rscript";
+ print $ofh "library(DEXSeq)\n";
+ print $ofh "samples_info = read.table(\"$samples_table_file\", header=T, row.names=1)\n";
+ print $ofh "dxd = DEXSeqDataSetFromHTSeq(as.vector(samples_info\$counts_filename), sampleData=samples_info, design = ~ sample + exon + condition:exon, flattenedfile=\"$genes_gtf_file.dexseq.gff\")\n";
+ print $ofh "dxd = estimateSizeFactors( dxd )\n";
+ print $ofh "dxd = estimateDispersions( dxd )\n";
+ print $ofh "plotDispEsts( dxd )\n";
+ print $ofh "dxd = testForDEU( dxd )\n";
+ print $ofh "dxd = estimateExonFoldChanges( dxd, fitExpToVar=\"condition\")\n";
+ print $ofh "dxr1 = DEXSeqResults( dxd )\n";
+ print $ofh "dxr1.sorted = dxr1[order(dxr1\$padj),]\n";
+ print $ofh "save(list = ls(all=TRUE), file = \"$out_prefix.Rdata\")\n";
+ print $ofh "write.table(apply(data.frame(dxr1.sorted), 2, as.character), file=\"$out_prefix.results.dat\", quote=F, sep=\"\t\")\n";
+
+ print $ofh "pdf(\"$out_prefix.pdf\")\n";
+
+ print $ofh "top_genes = unique(dxr1.sorted\$groupID[dxr1.sorted\$padj < 0.1 & ! is.na(dxr1.sorted\$padj)])\n";
+ print $ofh "top_genes = top_genes[1:min($top_genes_plot, length(top_genes))]\n";
+ print $ofh "message(\"Top $top_genes_plot genes: (\", paste(top_genes, collapse=','), \")\")\n";
+ print $ofh "for (gene in top_genes) { \n"
+ . " plotDEXSeq( dxr1 , gene, legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 , expression=FALSE, norCounts=TRUE, splicing=TRUE, displayTranscripts=TRUE)\n"
+ . "}\n";
+
+ #print $ofh "plotMA( dxr1, cex=0.8 )\n";
+ close $ofh;
+
+ }
+
+ $cmd = "R --no-save --no-restore --no-site-file --no-init-file -q < $dexseq_rscript";
+ $pipeliner->add_commands(new Command($cmd, "$analysis_token.dexseq.$top_genes_plot.ok"));
+
+ $pipeliner->run();
+
+
+}
+
+
+
+
+
+####
+sub parse_samples_file {
+ my ($samples_file) = @_;
+
+ my @samples_info;
+
+ my %seen;
+
+ open (my $fh, $samples_file) or die "Error, cannot open file: $samples_file";
+ while (<$fh>) {
+ if (/^\#/) { next; }
+ unless (/\w/) { next; }
+ chomp;
+ my $line = $_;
+ my @x = split(/\s+/);
+ my $condition = $x[0];
+ my $replicate = $x[1];
+ my $bam_filename = $x[2];
+
+ unless (-s $bam_filename) {
+ die "Error, cannot locate bam filename: $bam_filename as specified in samples file line: $line ";
+ }
+
+ if ($seen{$replicate}) {
+ die "Error, replicate name: [$replicate] must be unique among all replicate names. Please update your samples file";
+ }
+ $seen{$replicate} = 1;
+
+ push (@samples_info, [$condition, $replicate, $bam_filename]);
+ }
+ close $fh;
+
+ return(@samples_info);
+}
+
=====================================
Analysis/DifferentialExpression/run_GOseq.pl
=====================================
@@ -67,7 +67,7 @@ main: {
print $ofh "# capture list of genes for functional enrichment testing\n";
if ($genes_single_factor_file) {
- print $ofh "factor_labeling = read.table(\"$genes_single_factor_file\", row.names=1)\n";
+ print $ofh "factor_labeling = read.table(\"$genes_single_factor_file\", header=T, row.names=1)\n";
print $ofh "factor_labeling[,1] = rep('custom_list', dim(factor_labeling)[1])\n";
print $ofh "factor_labeling = factor_labeling[,1,drop=F]\n";
}
=====================================
Analysis/DifferentialExpression/sum_tech_replicates.pl
=====================================
@@ -0,0 +1,173 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+
+my $usage = <<__EOUSAGE__;
+
+#######################################################################
+#
+# Required:
+#
+# --matrix|m <string> replicates.TMM_normalized.fpkm.matrix
+#
+# --samples_file|s <string> description of sample-to-replicate mapping (tab-delimited)
+#
+# ex.
+# condA_br1 tech_condA_br1a
+# condA_br1 tech_condA_br1b
+# condA_br2 tech_condA_br2a
+# condA_br2 tech_condA_br2b
+#
+# --test|t write and execute on built-in test data
+#
+#
+#######################################################################
+
+
+__EOUSAGE__
+
+ ;
+
+
+my $matrix_file;
+my $use_avg_log_val = 0;
+my $samples_file;
+
+my $help_flag;
+
+my $test_flag = 0;
+
+&GetOptions("matrix|m=s" => \$matrix_file,
+ "samples_file|s=s" => \$samples_file,
+
+ "help|h" => \$help_flag,
+
+ "test|t" => \$test_flag,
+
+ );
+
+if ($help_flag) {
+ die $usage;
+}
+
+unless (($matrix_file && $samples_file) || $test_flag) {
+ die $usage;
+}
+
+
+main: {
+
+
+ if ($test_flag) {
+ $matrix_file = "test.matrix";
+ $samples_file = "test.samples";
+ &write_test_data($matrix_file, $samples_file);
+ }
+
+
+
+ my $out_prefix = "$matrix_file.sum_tech_reps";
+
+ my $out_matrix = $out_prefix . ".matrix";
+ my $out_rscript = $out_prefix . ".Rscript";
+
+ open (my $ofh, ">$out_rscript") or die "Error, cannot write to $out_rscript";
+ print $ofh <<__EORSCRIPT__;
+
+samples = read.table("$samples_file", header=F, check.names=F)
+sample_types = as.vector(unique(samples[,1]))
+nsamples = length(sample_types)
+
+data = read.table("$matrix_file", header=T, row.names=1, com='', nrows=10000, check.names=F)
+classes = sapply(data,class)
+data = read.table("$matrix_file", header=T, row.names=1, com='', colClasses=classes, check.names=F)
+data = as.matrix(data)
+sample_factoring = rep(NA, ncol(data))
+sample_expr_matrix = matrix(ncol=nsamples, nrow=nrow(data))
+colnames(sample_expr_matrix) = sample_types
+rownames(sample_expr_matrix) = rownames(data)
+
+for (i in 1:nsamples) {
+ sample_type = sample_types[i]
+ rep_indices = samples[,1] \%in% sample_type
+ #print(paste("rep_indices:", rep_indices))
+ rep_names = as.vector(samples[rep_indices,2])
+ cat("sample_type: ", sample_type, "\n")
+ cat("rep_names: ", rep_names, "\n")
+ col_indices = colnames(data) \%in% rep_names
+ #print(col_indices);
+ if (sum(col_indices) == 0) {
+ stop(cat("Error, no columns found matching sample type:", sample_type, "with replicate names:", rep_names))
+ }
+ if (sum(col_indices) != length(rep_names)) {
+ found_colnames = colnames(data)[col_indices]
+ missing = rep_names[ ! rep_names \%in% found_colnames]
+ cat ("Error, not all replicates accounted for. Found only", sum(col_indices), "columns but have", length(rep_names), "replicates:", rep_names, "for sample:", sample_type, "missing:", missing)
+ stop()
+ }
+ sample_factoring[col_indices] = sample_type
+ sum_vals = apply(data[,col_indices, drop=F], 1, sum)
+ sample_expr_matrix[,i] = sprintf("%.1f", sum_vals)
+}
+
+write.table(sample_expr_matrix, "$out_matrix", quote=F, sep="\t")
+
+__EORSCRIPT__
+
+;
+
+ my $cmd = "R --no-save --no-restore --no-site-file --no-init-file -q < $out_rscript";
+ my $ret = system($cmd);
+ if ($ret) {
+ die "Error, cmd: $cmd died with ret $ret";
+ }
+
+
+ print "\n\nDone. See output: $out_matrix\n\n";
+
+ exit(0);
+}
+
+
+####
+sub write_test_data {
+ my ($test_matrix_file, $test_samples_file) = @_;
+
+ open (my $ofh, ">$test_matrix_file") or die $!;
+ print $ofh
+"S1 S2 S3 S4 S5 C1 C2 C3 C4 C5
+1 456 726 380 554 184 9 7 3 9 7
+2 34 49 43 35 30 18 15 11 23 7
+3 22 17 35 17 18 45 127 73 78 93
+4 11 6 11 4 7 52 57 44 27 19
+5 18 19 12 25 17 193 130 69 137 164
+6 41 71 38 59 36 37 45 24 41 16
+7 2 11 17 12 10 152 230 137 185 154
+8 6 20 26 25 22 2 4 0 1 2
+9 12 28 11 13 16 4 15 6 12 12
+10 34 31 13 30 25 8 3 10 12 16
+";
+
+ close $ofh;
+
+
+ open ($ofh, ">$test_samples_file") or die $!;
+ print $ofh
+"S S1
+S S2
+S S3
+S S4
+S S5
+C C1
+C C2
+C C3
+C C4
+C C5
+";
+
+ return;
+}
+
=====================================
Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
=====================================
@@ -140,7 +140,15 @@ def main():
default="",
help="options to pass through to STAR's genomeGenerate function. ie. might need: --genomeChrBinNbits to log2[SequenceLength/NumberOfContigs] ",
)
-
+
+
+ parser.add_argument(
+ "--STAR_genomeAlign_opts",
+ type=str,
+ default="",
+ help="options to pass through to STAR's alignment function. ",
+ )
+
args = parser.parse_args()
PICARD_HOME = os.getenv("PICARD_HOME")
@@ -277,6 +285,7 @@ def main():
+ " --alignSJDBoverhangMin 10 "
+ " --outSAMtype BAM SortedByCoordinate "
+ " --limitBAMsortRAM {} ".format(args.maxram)
+ + " {} ".format(args.STAR_genomeAlign_opts)
+ " --readFilesIn "
+ " ".join(reads_paths)
)
@@ -284,6 +293,8 @@ def main():
if re.search("\.gz$", reads_paths[0]):
cmd += " --readFilesCommand 'gunzip -c' "
+
+
pipeliner.add_commands([Pipeliner.Command(cmd, "star_aln.ok")])
pipeliner.run()
=====================================
Changelog.txt
=====================================
@@ -1,3 +1,15 @@
+
+# Trinity-v2.15.2 July 31, 2024
+- updated docker (and apptainer/singularity) to ubuntu 24.04
+- bamsifter compilation issue addressed
+- minor updates to accessory scripts
+
+
+# Trinity-v2.15.1 Feb 5, 2023
+- bamsifter update to ease compilation issues
+- update to contig_ExN50_statistic.pl to provide either transcript (default) or gene based analysis (note, both use the isoform expression matrix!)
+- inclusion of try_estimate_TPM_filtering_threshold.Rscript, which tries to estimate the count of transcripts with sufficient expression.
+
# Trinity-v2.15.0 Nov 30, 2022
- use DB_File for storing read names wanted during normalization step eliminating excessive RAM usage.
- support for hpc_gridrunner/singularity
=====================================
Docker/Dockerfile
=====================================
@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:24.04
MAINTAINER bhaas at broadinstitute.org
ENV DEBIAN_FRONTEND=noninteractive
@@ -42,7 +42,6 @@ RUN apt-get -qq update && apt-get -qq -y install \
pkg-config \
python3 \
python3-dev \
- python3-distutils \
python3-pip \
python3-setuptools \
rsync \
@@ -77,7 +76,7 @@ WORKDIR $SRC
RUN apt-get install -y texlive texlive-latex-extra
-ENV R_VERSION=R-4.2.0
+ENV R_VERSION=R-4.4.0
RUN curl https://cran.r-project.org/src/base/R-4/$R_VERSION.tar.gz -o $R_VERSION.tar.gz && \
tar xvf $R_VERSION.tar.gz && \
@@ -112,9 +111,9 @@ RUN apt-get install -y cython3
RUN ln -sf /usr/bin/python3 /usr/bin/python
## some python modules
-RUN pip3 install numpy
-RUN pip3 install git+https://github.com/ewels/MultiQC.git
-RUN pip3 install HTSeq
+#RUN pip3 install numpy
+#RUN pip3 install git+https://github.com/ewels/MultiQC.git
+#RUN pip3 install HTSeq
## bowtie
@@ -234,16 +233,30 @@ RUN STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz"
## Salmon
WORKDIR $SRC
-ENV SALMON_VERSION=1.5.2
-RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
- tar xvf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
- ln -s $SRC/salmon-${SALMON_VERSION}_linux_x86_64/bin/salmon $BIN/.
+ENV SALMON_VERSION=1.10.0
+RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz -O salmon-1.10.0_linux_x86_64.tar.gz && \
+ tar xvf salmon-1.10.0_linux_x86_64.tar.gz && \
+ ln -s $SRC/salmon-latest_linux_x86_64/bin/salmon $BIN/.
+
+
+## autoconf 2.69 needed for trinity installed verison of htslib
+WORKDIR $SRC
+RUN wget http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz && \
+ tar xf autoconf* && \
+ cd autoconf-2.69 && \
+ sh configure --prefix /usr/local && \
+ make install
+
+
+RUN apt-get install -y python3-numpy git
+RUN pip3 install git+https://github.com/ewels/MultiQC.git --break-system-packages
+RUN pip3 install HTSeq --break-system-packages
## Trinity
WORKDIR $SRC
-ENV TRINITY_VERSION="2.15.1"
-ENV TRINITY_CO=8f0c44bccc321170b0994b2196f5be27f9c49b10
+ENV TRINITY_VERSION="2.15.2"
+ENV TRINITY_CO=4be803497fd22ce8461a9637eff46bc3b75a594a
WORKDIR $SRC
=====================================
Docker/README.md
=====================================
@@ -8,3 +8,44 @@
--max_memory 1G --CPU 4 --output `pwd`/trinity_out_dir
+
+
+# If you need to install Singularity on linux
+
+
+sudo apt-get update && \
+sudo apt-get install -y build-essential \
+libseccomp-dev pkg-config squashfs-tools cryptsetup
+
+sudo rm -r /usr/local/go
+
+export VERSION=1.13.15 OS=linux ARCH=amd64 # change this as you need
+
+wget -O /tmp/go${VERSION}.${OS}-${ARCH}.tar.gz https://dl.google.com/go/go${VERSION}.${OS}-${ARCH}.tar.gz && \
+sudo tar -C /usr/local -xzf /tmp/go${VERSION}.${OS}-${ARCH}.tar.gz
+
+echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
+echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
+source ~/.bashrc
+
+curl -sfL https://install.goreleaser.com/github.com/golangci/golangci-lint.sh |
+sh -s -- -b $(go env GOPATH)/bin v1.21.0
+
+mkdir -p ${GOPATH}/src/github.com/sylabs && \
+cd ${GOPATH}/src/github.com/sylabs && \
+git clone https://github.com/sylabs/singularity.git && \
+cd singularity
+
+git checkout v3.6.3
+
+cd ${GOPATH}/src/github.com/sylabs/singularity && \
+./mconfig && \
+cd ./builddir && \
+make && \
+sudo make install
+
+singularity version
+
+# as per: https://github.com/apptainer/singularity/issues/5099#issuecomment-1286798317
+
+
=====================================
README.md
=====================================
@@ -1,10 +1,7 @@
trinityrnaseq
=============
-[](https://travis-ci.org/trinityrnaseq/trinityrnaseq)
-[](https://bioconda.github.io/recipes/trinity/README.html)
-
-Trinity RNA-Seq de novo transcriptome assembly see the main webpage [http://trinityrnaseq.github.io](http://trinityrnaseq.github.io)
+Trinity RNA-Seq de novo transcriptome assembly see the Trinity [wiki](https://github.com/trinityrnaseq/trinityrnaseq/wiki)
## Contributing
=====================================
Trinity
=====================================
@@ -22,7 +22,7 @@ use Data::Dumper;
-my $VERSION = "Trinity-v2.15.1";
+my $VERSION = "Trinity-v2.15.2";
#my $VERSION = "__BLEEDING_EDGE__";
=====================================
trinity-plugins/ParaFly/Makefile
=====================================
@@ -98,12 +98,12 @@ DIST_ARCHIVES = $(distdir).tar.gz
GZIP_ENV = --best
distuninstallcheck_listfiles = find . -type f -print
distcleancheck_listfiles = find . -type f -print
-ACLOCAL = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run aclocal-1.11
-AMTAR = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run tar
+ACLOCAL = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run tar
AM_CXXFLAGS = -pedantic -Wall -Wextra -Wno-long-long -Wno-deprecated -m64
-AUTOCONF = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoconf
-AUTOHEADER = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoheader
-AUTOMAKE = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run automake-1.11
+AUTOCONF = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run automake-1.11
AWK = gawk
CPPFLAGS =
CXX = g++
@@ -125,7 +125,7 @@ LDFLAGS =
LIBOBJS =
LIBS =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run makeinfo
MKDIR_P = /usr/bin/mkdir -p
OBJEXT = o
PACKAGE = parafly
@@ -136,13 +136,13 @@ PACKAGE_TARNAME = parafly
PACKAGE_VERSION = 0.1
PATH_SEPARATOR = :
SET_MAKE =
-SHELL = /bin/sh
+SHELL = /bin/bash
STRIP =
VERSION = 0.1
-abs_builddir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
-abs_srcdir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
-abs_top_builddir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
-abs_top_srcdir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
+abs_builddir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
+abs_srcdir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
+abs_top_builddir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
+abs_top_srcdir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
ac_ct_CXX =
am__include = include
am__leading_dot = .
@@ -161,7 +161,7 @@ host_alias =
htmldir = ${docdir}
includedir = ${prefix}/include
infodir = ${datarootdir}/info
-install_sh = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/install-sh
+install_sh = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
@@ -170,7 +170,7 @@ mandir = ${datarootdir}/man
mkdir_p = /usr/bin/mkdir -p
oldincludedir = /usr/include
pdfdir = ${docdir}
-prefix = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
+prefix = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
program_transform_name = s,x,x,
psdir = ${docdir}
sbindir = ${exec_prefix}/sbin
=====================================
trinity-plugins/ParaFly/bin/ParaFly
=====================================
Binary files a/trinity-plugins/ParaFly/bin/ParaFly and b/trinity-plugins/ParaFly/bin/ParaFly differ
=====================================
trinity-plugins/ParaFly/config.log
=====================================
@@ -4,17 +4,17 @@ running configure, to aid debugging if configure makes a mistake.
It was created by Parafly configure 0.1, which was
generated by GNU Autoconf 2.69. Invocation command line was
- $ ./configure --prefix=/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly CXX=g++ CC=gcc CFLAGS=-fopenmp CXXFLAGS=-fopenmp
+ $ ./configure --prefix=/home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly CXX=g++ CC=gcc CFLAGS=-fopenmp CXXFLAGS=-fopenmp
## --------- ##
## Platform. ##
## --------- ##
-hostname = methods01.broadinstitute.org
+hostname = bhaas-gce2
uname -m = x86_64
-uname -r = 3.10.0-1160.15.2.el7.x86_64
+uname -r = 5.15.0-1062-gcp
uname -s = Linux
-uname -v = #1 SMP Thu Jan 21 16:15:07 EST 2021
+uname -v = #70~20.04.1-Ubuntu SMP Fri May 24 20:12:18 UTC 2024
/usr/bin/uname -p = x86_64
/bin/uname -X = unknown
@@ -27,124 +27,113 @@ uname -v = #1 SMP Thu Jan 21 16:15:07 EST 2021
/usr/bin/oslevel = unknown
/bin/universe = unknown
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/cmake_3.18.3/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/autoconf_2.69/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/perl_5.28.0/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/mysql_5.6.20/bin
-PATH: /broad/software/nonfree/Linux/redhat_7_x86_64/pkgs/oracle_instantclient-11.2.0.4.0/instantclient_11_2
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/google-cloud-sdk/bin
-PATH: /home/unix/bhaas/miniconda2/envs/py3/bin
-PATH: /home/unix/bhaas/miniconda2/condabin
-PATH: /home/unix/bhaas/utilities/emboss
-PATH: .
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/hmmer_3.1/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/git_2.12.0/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/jdk1.8.0_345/bin
-PATH: /broad/software/free/Linux/redhat_7_x86_64/pkgs/ncbi-blast_2.2.30+-x86_64/bin
-PATH: /broad/uge/8.5.5/bin/lx-amd64
-PATH: /home/unix/bhaas/utilities
-PATH: /home/unix/bhaas/GITHUB/pasapipeline/misc_utilities/
-PATH: /home/unix/bhaas/bin
-PATH: /seq/regev_genome_portal/SOFTWARE/SRA_TOOLKIT/sratoolkit.2.5.1-centos_linux64/bin
-PATH: /usr/local/bin
-PATH: /usr/bin
+PATH: /home/bhaas/utilities
+PATH: /home/bhaas/BIN
+PATH: /usr/local/go/bin
+PATH: /home/bhaas/mambaforge/bin
+PATH: /opt/mamba/condabin
PATH: /usr/local/sbin
+PATH: /usr/local/bin
PATH: /usr/sbin
-PATH: /opt/puppetlabs/bin
-PATH: /opt/dell/srvadmin/bin
-PATH: /home/unix/bhaas/.local/bin
-PATH: /seq/RNASEQ/TOOLS/SPADES/SPAdes-3.14.1-Linux/bin
-PATH: /seq/regev_genome_portal/SOFTWARE/OpenMPI/openmpi-1.6.5/bin
-PATH: /home/unix/bhaas/GITHUB/Trinity_CTAT/fusion
-PATH: /home/unix/bhaas/GITHUB/trinityrnaseq
-PATH: /home/unix/bhaas/.firecloud-cli/ubin
+PATH: /usr/bin
+PATH: /sbin
+PATH: /bin
+PATH: /usr/games
+PATH: /usr/local/games
+PATH: /snap/bin
+PATH: /home/bhaas/GITHUB/trinityrnaseq
+PATH: /home/bhaas/go/bin
+PATH: /home/bhaas/SOFTWARE/gatk-4.1.9.0
## ----------- ##
## Core tests. ##
## ----------- ##
-configure:1884: checking for a BSD-compatible install
-configure:1952: result: /usr/bin/install -c
-configure:1963: checking whether build environment is sane
-configure:2013: result: yes
-configure:2154: checking for a thread-safe mkdir -p
-configure:2193: result: /usr/bin/mkdir -p
-configure:2206: checking for gawk
-configure:2222: found /usr/bin/gawk
-configure:2233: result: gawk
-configure:2244: checking whether make sets $(MAKE)
-configure:2266: result: yes
-configure:2464: checking for C++ compiler version
-configure:2473: g++ --version >&5
-g++ (GCC) 5.2.0
-Copyright (C) 2015 Free Software Foundation, Inc.
+configure:1880: checking for a BSD-compatible install
+configure:1948: result: /usr/bin/install -c
+configure:1959: checking whether build environment is sane
+configure:2009: result: yes
+configure:2150: checking for a thread-safe mkdir -p
+configure:2189: result: /usr/bin/mkdir -p
+configure:2202: checking for gawk
+configure:2218: found /usr/bin/gawk
+configure:2229: result: gawk
+configure:2240: checking whether make sets $(MAKE)
+configure:2262: result: yes
+configure:2460: checking for C++ compiler version
+configure:2469: g++ --version >&5
+g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-configure:2484: $? = 0
-configure:2473: g++ -v >&5
+configure:2480: $? = 0
+configure:2469: g++ -v >&5
Using built-in specs.
COLLECT_GCC=g++
-COLLECT_LTO_WRAPPER=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0/libexec/gcc/x86_64-redhat-linux/5.2.0/lto-wrapper
-Target: x86_64-redhat-linux
-Configured with: /tmp/redhat_7_x86_64/build/tmp/gcc-5.2.0/configure --prefix=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0 --enable-lto --with-cloog --enable-plugins --enable-languages=c,c++,objc,obj-c++,fortran --build=x86_64-redhat-linux --disable-multilib --with-gmp=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0 --with-mpfr=/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_5.2.0
+COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
+OFFLOAD_TARGET_NAMES=nvptx-none:hsa
+OFFLOAD_TARGET_DEFAULT=1
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.4.0-1ubuntu1~20.04.2' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-9QDOt0/gcc-9-9.4.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
-gcc version 5.2.0 (GCC)
-configure:2484: $? = 0
-configure:2473: g++ -V >&5
+gcc version 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.2)
+configure:2480: $? = 0
+configure:2469: g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
-configure:2484: $? = 1
-configure:2473: g++ -qversion >&5
-g++: error: unrecognized command line option '-qversion'
+configure:2480: $? = 1
+configure:2469: g++ -qversion >&5
+g++: error: unrecognized command line option '-qversion'; did you mean '--version'?
g++: fatal error: no input files
compilation terminated.
-configure:2484: $? = 1
-configure:2504: checking whether the C++ compiler works
-configure:2526: g++ -fopenmp conftest.cpp >&5
-configure:2530: $? = 0
-configure:2578: result: yes
-configure:2581: checking for C++ compiler default output file name
-configure:2583: result: a.out
-configure:2589: checking for suffix of executables
-configure:2596: g++ -o conftest -fopenmp conftest.cpp >&5
-configure:2600: $? = 0
-configure:2622: result:
-configure:2644: checking whether we are cross compiling
-configure:2652: g++ -o conftest -fopenmp conftest.cpp >&5
-configure:2656: $? = 0
-configure:2663: ./conftest
-configure:2667: $? = 0
-configure:2682: result: no
-configure:2687: checking for suffix of object files
-configure:2709: g++ -c -fopenmp conftest.cpp >&5
-configure:2713: $? = 0
-configure:2734: result: o
-configure:2738: checking whether we are using the GNU C++ compiler
-configure:2757: g++ -c -fopenmp conftest.cpp >&5
-configure:2757: $? = 0
-configure:2766: result: yes
-configure:2775: checking whether g++ accepts -g
-configure:2795: g++ -c -g conftest.cpp >&5
-configure:2795: $? = 0
-configure:2836: result: yes
-configure:2870: checking for style of include used by make
-configure:2898: result: GNU
-configure:2923: checking dependency style of g++
-configure:3033: result: gcc3
-configure:3057: checking for g++ option to support OpenMP
-configure:3072: g++ -o conftest -fopenmp conftest.cpp >&5
-configure:3072: $? = 0
-configure:3104: result: none needed
-configure:3125: checking for library containing cos
-configure:3156: g++ -o conftest -fopenmp conftest.cpp >&5
-configure:3156: $? = 0
-configure:3173: result: none required
-configure:3315: creating ./config.status
+configure:2480: $? = 1
+configure:2500: checking whether the C++ compiler works
+configure:2522: g++ -fopenmp conftest.cpp >&5
+configure:2526: $? = 0
+configure:2574: result: yes
+configure:2577: checking for C++ compiler default output file name
+configure:2579: result: a.out
+configure:2585: checking for suffix of executables
+configure:2592: g++ -o conftest -fopenmp conftest.cpp >&5
+configure:2596: $? = 0
+configure:2618: result:
+configure:2640: checking whether we are cross compiling
+configure:2648: g++ -o conftest -fopenmp conftest.cpp >&5
+configure:2652: $? = 0
+configure:2659: ./conftest
+configure:2663: $? = 0
+configure:2651: result: no
+configure:2656: checking for suffix of object files
+configure:2678: g++ -c -fopenmp conftest.cpp >&5
+configure:2682: $? = 0
+configure:2703: result: o
+configure:2707: checking whether we are using the GNU C++ compiler
+configure:2726: g++ -c -fopenmp conftest.cpp >&5
+configure:2726: $? = 0
+configure:2735: result: yes
+configure:2744: checking whether g++ accepts -g
+configure:2764: g++ -c -g conftest.cpp >&5
+configure:2764: $? = 0
+configure:2805: result: yes
+configure:2839: checking for style of include used by make
+configure:2867: result: GNU
+configure:2892: checking dependency style of g++
+configure:3002: result: gcc3
+configure:3026: checking for g++ option to support OpenMP
+configure:3041: g++ -o conftest -fopenmp conftest.cpp >&5
+configure:3041: $? = 0
+configure:3073: result: none needed
+configure:3094: checking for library containing cos
+configure:3125: g++ -o conftest -fopenmp conftest.cpp >&5
+conftest.cpp:18:6: warning: declaration of 'char cos()' conflicts with built-in declaration 'double cos(double)' [-Wbuiltin-declaration-mismatch]
+ 18 | char cos ();
+ | ^~~
+configure:3125: $? = 0
+configure:3142: result: none required
+configure:3276: creating ./config.status
## ---------------------- ##
## Running config.status. ##
@@ -159,13 +148,13 @@ generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_COMMANDS =
$ ./config.status
-on methods01.broadinstitute.org
+on bhaas-gce2
-config.status:838: creating Makefile
-config.status:838: creating src/Makefile
-config.status:838: creating config.h
-config.status:1019: config.h is unchanged
-config.status:1067: executing depfiles commands
+config.status:834: creating Makefile
+config.status:834: creating src/Makefile
+config.status:834: creating config.h
+config.status:1015: config.h is unchanged
+config.status:1063: executing depfiles commands
## ---------------- ##
## Cache variables. ##
@@ -204,15 +193,15 @@ am_cv_CXX_dependencies_compiler_type=gcc3
## Output variables. ##
## ----------------- ##
-ACLOCAL='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run aclocal-1.11'
+ACLOCAL='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run aclocal-1.11'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
-AMTAR='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run tar'
+AMTAR='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run tar'
AM_CXXFLAGS='-pedantic -Wall -Wextra -Wno-long-long -Wno-deprecated -m64'
-AUTOCONF='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoconf'
-AUTOHEADER='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoheader'
-AUTOMAKE='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run automake-1.11'
+AUTOCONF='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoconf'
+AUTOHEADER='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoheader'
+AUTOMAKE='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run automake-1.11'
AWK='gawk'
CPPFLAGS=''
CXX='g++'
@@ -233,7 +222,7 @@ LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
-MAKEINFO='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run makeinfo'
+MAKEINFO='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run makeinfo'
MKDIR_P='/usr/bin/mkdir -p'
OBJEXT='o'
OPENMP_CXXFLAGS=''
@@ -246,7 +235,7 @@ PACKAGE_URL=''
PACKAGE_VERSION='0.1'
PATH_SEPARATOR=':'
SET_MAKE=''
-SHELL='/bin/sh'
+SHELL='/bin/bash'
STRIP=''
VERSION='0.1'
ac_ct_CXX=''
@@ -271,7 +260,7 @@ host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
-install_sh='${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/install-sh'
+install_sh='${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
@@ -280,7 +269,7 @@ mandir='${datarootdir}/man'
mkdir_p='/usr/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
-prefix='/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly'
+prefix='/home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly'
program_transform_name='s,x,x,'
psdir='${docdir}'
runstatedir='${localstatedir}/run'
=====================================
trinity-plugins/ParaFly/config.status
=====================================
@@ -1,4 +1,4 @@
-#! /bin/sh
+#! /bin/bash
# Generated by configure.
# Run this file to recreate the current configuration.
# Compiler output produced by configure, useful for debugging
@@ -8,7 +8,7 @@ debug=false
ac_cs_recheck=false
ac_cs_silent=false
-SHELL=${CONFIG_SHELL-/bin/sh}
+SHELL=${CONFIG_SHELL-/bin/bash}
export SHELL
## -------------------- ##
## M4sh Initialization. ##
@@ -427,7 +427,7 @@ $config_commands
Report bugs to <bug-report at address>."
-ac_cs_config="'--prefix=/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly' 'CXX=g++' 'CC=gcc' 'CFLAGS=-fopenmp' 'CXXFLAGS=-fopenmp'"
+ac_cs_config="'--prefix=/home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly' 'CXX=g++' 'CC=gcc' 'CFLAGS=-fopenmp' 'CXXFLAGS=-fopenmp'"
ac_cs_version="\
Parafly config.status 0.1
configured by ./configure, generated by GNU Autoconf 2.69,
@@ -437,7 +437,7 @@ Copyright (C) 2012 Free Software Foundation, Inc.
This config.status script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it."
-ac_pwd='/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly'
+ac_pwd='/home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly'
srcdir='.'
INSTALL='/usr/bin/install -c'
MKDIR_P='/usr/bin/mkdir -p'
@@ -519,10 +519,10 @@ if $ac_cs_silent; then
fi
if $ac_cs_recheck; then
- set X /bin/sh './configure' '--prefix=/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly' 'CXX=g++' 'CC=gcc' 'CFLAGS=-fopenmp' 'CXXFLAGS=-fopenmp' $ac_configure_extra_args --no-create --no-recursion
+ set X /bin/bash './configure' '--prefix=/home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly' 'CXX=g++' 'CC=gcc' 'CFLAGS=-fopenmp' 'CXXFLAGS=-fopenmp' $ac_configure_extra_args --no-create --no-recursion
shift
- $as_echo "running CONFIG_SHELL=/bin/sh $*" >&6
- CONFIG_SHELL='/bin/sh'
+ $as_echo "running CONFIG_SHELL=/bin/bash $*" >&6
+ CONFIG_SHELL='/bin/bash'
export CONFIG_SHELL
exec "$@"
fi
@@ -639,7 +639,7 @@ S["CXXFLAGS"]="-fopenmp"
S["CXX"]="g++"
S["am__untar"]="${AMTAR} xf -"
S["am__tar"]="${AMTAR} chof - \"$$tardir\""
-S["AMTAR"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run tar"
+S["AMTAR"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run tar"
S["am__leading_dot"]="."
S["SET_MAKE"]=""
S["AWK"]="gawk"
@@ -647,12 +647,12 @@ S["mkdir_p"]="/usr/bin/mkdir -p"
S["MKDIR_P"]="/usr/bin/mkdir -p"
S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s"
S["STRIP"]=""
-S["install_sh"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/install-sh"
-S["MAKEINFO"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run makeinfo"
-S["AUTOHEADER"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoheader"
-S["AUTOMAKE"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run automake-1.11"
-S["AUTOCONF"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoconf"
-S["ACLOCAL"]="${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run aclocal-1.11"
+S["install_sh"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/install-sh"
+S["MAKEINFO"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run makeinfo"
+S["AUTOHEADER"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoheader"
+S["AUTOMAKE"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run automake-1.11"
+S["AUTOCONF"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoconf"
+S["ACLOCAL"]="${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run aclocal-1.11"
S["VERSION"]="0.1"
S["PACKAGE"]="parafly"
S["CYGPATH_W"]="echo"
@@ -689,7 +689,7 @@ S["libexecdir"]="${exec_prefix}/libexec"
S["sbindir"]="${exec_prefix}/sbin"
S["bindir"]="${exec_prefix}/bin"
S["program_transform_name"]="s,x,x,"
-S["prefix"]="/broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly"
+S["prefix"]="/home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly"
S["exec_prefix"]="${prefix}"
S["PACKAGE_URL"]=""
S["PACKAGE_BUGREPORT"]="bug-report at address"
@@ -698,7 +698,7 @@ S["PACKAGE_VERSION"]="0.1"
S["PACKAGE_TARNAME"]="parafly"
S["PACKAGE_NAME"]="Parafly"
S["PATH_SEPARATOR"]=":"
-S["SHELL"]="/bin/sh"
+S["SHELL"]="/bin/bash"
_ACAWK
cat >>"$ac_tmp/subs1.awk" <<_ACAWK &&
for (key in S) S_is_set[key] = 1
=====================================
trinity-plugins/ParaFly/src/.deps/ParaFly.Po
=====================================
@@ -1,511 +1,631 @@
ParaFly.o: ParaFly.cpp /usr/include/stdc-predef.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/iostream \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/c++config.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/os_defines.h \
- /usr/include/features.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/cpu_defines.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ostream \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ios \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/iosfwd \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stringfwd.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/memoryfwd.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/postypes.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cwchar \
- /usr/include/wchar.h /usr/include/stdio.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/lib/gcc/x86_64-redhat-linux/7.3.0/include/stdarg.h \
- /usr/include/bits/wchar.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/lib/gcc/x86_64-redhat-linux/7.3.0/include/stddef.h \
- /usr/include/xlocale.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/exception \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/exception.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/exception_ptr.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/exception_defines.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/cxxabi_init_exception.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/typeinfo \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/hash_bytes.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/new \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/nested_exception.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/move.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/concept_check.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/type_traits \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/char_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_algobase.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/functexcept.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/cpp_type_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/type_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/numeric_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_pair.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_iterator_base_types.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_iterator_base_funcs.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/debug/assertions.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_iterator.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/ptr_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/debug/debug.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/predefined_ops.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cstdint \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/lib/gcc/x86_64-redhat-linux/7.3.0/include/stdint.h \
- /usr/include/stdint.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/localefwd.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/c++locale.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/clocale \
- /usr/include/locale.h /usr/include/bits/locale.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cctype \
- /usr/include/ctype.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/bits/byteswap-16.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/ios_base.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/atomicity.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/gthr.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/gthr-default.h \
- /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
- /usr/include/bits/sched.h /usr/include/bits/time.h \
- /usr/include/bits/timex.h /usr/include/bits/pthreadtypes.h \
- /usr/include/bits/setjmp.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/atomic_word.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/locale_classes.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/string \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/allocator.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/c++allocator.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/new_allocator.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/ostream_insert.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/cxxabi_forced.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_function.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/backward/binders.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/range_access.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/initializer_list \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/basic_string.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/alloc_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/alloc_traits.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/string_conversions.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cstdlib \
- /usr/include/stdlib.h /usr/include/bits/waitflags.h \
- /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
- /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
- /usr/include/alloca.h /usr/include/bits/stdlib-float.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/std_abs.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cstdio \
- /usr/include/libio.h /usr/include/_G_config.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cerrno \
- /usr/include/errno.h /usr/include/bits/errno.h \
- /usr/include/linux/errno.h /usr/include/asm/errno.h \
+ /usr/include/c++/9/iostream \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/c++config.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/os_defines.h \
+ /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \
+ /usr/include/x86_64-linux-gnu/bits/wordsize.h \
+ /usr/include/x86_64-linux-gnu/bits/long-double.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/cpu_defines.h \
+ /usr/include/c++/9/ostream /usr/include/c++/9/ios \
+ /usr/include/c++/9/iosfwd /usr/include/c++/9/bits/stringfwd.h \
+ /usr/include/c++/9/bits/memoryfwd.h /usr/include/c++/9/bits/postypes.h \
+ /usr/include/c++/9/cwchar /usr/include/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/libc-header-start.h \
+ /usr/include/x86_64-linux-gnu/bits/floatn.h \
+ /usr/include/x86_64-linux-gnu/bits/floatn-common.h \
+ /usr/lib/gcc/x86_64-linux-gnu/9/include/stddef.h \
+ /usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h \
+ /usr/include/x86_64-linux-gnu/bits/wchar.h \
+ /usr/include/x86_64-linux-gnu/bits/types/wint_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/mbstate_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__FILE.h \
+ /usr/include/x86_64-linux-gnu/bits/types/FILE.h \
+ /usr/include/x86_64-linux-gnu/bits/types/locale_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__locale_t.h \
+ /usr/include/c++/9/exception /usr/include/c++/9/bits/exception.h \
+ /usr/include/c++/9/bits/exception_ptr.h \
+ /usr/include/c++/9/bits/exception_defines.h \
+ /usr/include/c++/9/bits/cxxabi_init_exception.h \
+ /usr/include/c++/9/typeinfo /usr/include/c++/9/bits/hash_bytes.h \
+ /usr/include/c++/9/new /usr/include/c++/9/bits/nested_exception.h \
+ /usr/include/c++/9/bits/move.h /usr/include/c++/9/bits/concept_check.h \
+ /usr/include/c++/9/type_traits /usr/include/c++/9/bits/char_traits.h \
+ /usr/include/c++/9/bits/stl_algobase.h \
+ /usr/include/c++/9/bits/functexcept.h \
+ /usr/include/c++/9/bits/cpp_type_traits.h \
+ /usr/include/c++/9/ext/type_traits.h \
+ /usr/include/c++/9/ext/numeric_traits.h \
+ /usr/include/c++/9/bits/stl_pair.h \
+ /usr/include/c++/9/bits/stl_iterator_base_types.h \
+ /usr/include/c++/9/bits/stl_iterator_base_funcs.h \
+ /usr/include/c++/9/debug/assertions.h \
+ /usr/include/c++/9/bits/stl_iterator.h \
+ /usr/include/c++/9/bits/ptr_traits.h /usr/include/c++/9/debug/debug.h \
+ /usr/include/c++/9/bits/predefined_ops.h /usr/include/c++/9/cstdint \
+ /usr/lib/gcc/x86_64-linux-gnu/9/include/stdint.h /usr/include/stdint.h \
+ /usr/include/x86_64-linux-gnu/bits/types.h \
+ /usr/include/x86_64-linux-gnu/bits/timesize.h \
+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
+ /usr/include/x86_64-linux-gnu/bits/time64.h \
+ /usr/include/x86_64-linux-gnu/bits/stdint-intn.h \
+ /usr/include/x86_64-linux-gnu/bits/stdint-uintn.h \
+ /usr/include/c++/9/bits/localefwd.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h \
+ /usr/include/c++/9/clocale /usr/include/locale.h \
+ /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/9/cctype \
+ /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/endianness.h \
+ /usr/include/c++/9/bits/ios_base.h /usr/include/c++/9/ext/atomicity.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/gthr.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/types/time_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_timespec.h \
+ /usr/include/x86_64-linux-gnu/bits/sched.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_sched_param.h \
+ /usr/include/x86_64-linux-gnu/bits/cpu-set.h /usr/include/time.h \
+ /usr/include/x86_64-linux-gnu/bits/time.h \
+ /usr/include/x86_64-linux-gnu/bits/timex.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_timeval.h \
+ /usr/include/x86_64-linux-gnu/bits/types/clock_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \
+ /usr/include/x86_64-linux-gnu/bits/types/clockid_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/timer_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/thread-shared-types.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes-arch.h \
+ /usr/include/x86_64-linux-gnu/bits/struct_mutex.h \
+ /usr/include/x86_64-linux-gnu/bits/struct_rwlock.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \
+ /usr/include/c++/9/bits/locale_classes.h /usr/include/c++/9/string \
+ /usr/include/c++/9/bits/allocator.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/c++allocator.h \
+ /usr/include/c++/9/ext/new_allocator.h \
+ /usr/include/c++/9/bits/ostream_insert.h \
+ /usr/include/c++/9/bits/cxxabi_forced.h \
+ /usr/include/c++/9/bits/stl_function.h \
+ /usr/include/c++/9/backward/binders.h \
+ /usr/include/c++/9/bits/range_access.h \
+ /usr/include/c++/9/initializer_list \
+ /usr/include/c++/9/bits/basic_string.h \
+ /usr/include/c++/9/ext/alloc_traits.h \
+ /usr/include/c++/9/bits/alloc_traits.h \
+ /usr/include/c++/9/ext/string_conversions.h /usr/include/c++/9/cstdlib \
+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/uintn-identity.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/types/sigset_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__sigset_t.h \
+ /usr/include/alloca.h /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/c++/9/bits/std_abs.h /usr/include/c++/9/cstdio \
+ /usr/include/stdio.h /usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__fpos64_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_FILE.h \
+ /usr/include/x86_64-linux-gnu/bits/types/cookie_io_functions_t.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/c++/9/cerrno /usr/include/errno.h \
+ /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/x86_64-linux-gnu/asm/errno.h \
/usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/functional_hash.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/basic_string.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/locale_classes.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/system_error \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/error_constants.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/stdexcept \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/streambuf \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/streambuf.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/basic_ios.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/locale_facets.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cwctype \
- /usr/include/wctype.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/ctype_base.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/streambuf_iterator.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/ctype_inline.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/locale_facets.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/basic_ios.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/ostream.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/istream \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/istream.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/fstream \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/codecvt.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/basic_file.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/c++io.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/fstream.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/sstream \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/sstream.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/lib/gcc/x86_64-redhat-linux/7.3.0/include/omp.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/vector \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_construct.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_uninitialized.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_vector.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_bvector.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/vector.tcc \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/map \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_tree.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/aligned_buffer.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_map.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/tuple \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/utility \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_relops.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/array \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/uses_allocator.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/invoke.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_multimap.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/algorithm \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_algo.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/algorithmfwd.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_heap.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_tempbuf.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/uniform_int_dist.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/limits \
- /usr/include/signal.h /usr/include/bits/signum.h \
- /usr/include/bits/siginfo.h /usr/include/bits/sigaction.h \
- /usr/include/bits/sigcontext.h /usr/include/bits/sigstack.h \
- /usr/include/sys/ucontext.h /usr/include/bits/sigthread.h \
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argProcessor.hpp:
=====================================
trinity-plugins/ParaFly/src/.deps/argProcessor.Po
=====================================
@@ -1,362 +1,452 @@
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- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/localefwd.h \
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- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/iosfwd \
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- /usr/include/bits/sched.h /usr/include/bits/time.h \
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- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/atomic_word.h \
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- /usr/include/errno.h /usr/include/bits/errno.h \
- /usr/include/linux/errno.h /usr/include/asm/errno.h \
+ argProcessor.hpp /usr/include/c++/9/map \
+ /usr/include/c++/9/bits/stl_tree.h \
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+ /usr/include/x86_64-linux-gnu/bits/long-double.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs.h \
+ /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/cpu_defines.h \
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+ /usr/include/x86_64-linux-gnu/bits/floatn-common.h \
+ /usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h \
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+ /usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__FILE.h \
+ /usr/include/x86_64-linux-gnu/bits/types/FILE.h \
+ /usr/include/x86_64-linux-gnu/bits/types/locale_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__locale_t.h \
+ /usr/include/c++/9/cstdint \
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+ /usr/include/x86_64-linux-gnu/bits/typesizes.h \
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+ /usr/include/c++/9/cctype /usr/include/ctype.h \
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+ /usr/include/pthread.h /usr/include/sched.h \
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+ /usr/include/x86_64-linux-gnu/bits/types/clock_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_tm.h \
+ /usr/include/x86_64-linux-gnu/bits/types/clockid_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/timer_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
+ /usr/include/x86_64-linux-gnu/bits/thread-shared-types.h \
+ /usr/include/x86_64-linux-gnu/bits/pthreadtypes-arch.h \
+ /usr/include/x86_64-linux-gnu/bits/struct_mutex.h \
+ /usr/include/x86_64-linux-gnu/bits/struct_rwlock.h \
+ /usr/include/x86_64-linux-gnu/bits/setjmp.h \
+ /usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h \
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+ /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
+ /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
+ /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/endian.h \
+ /usr/include/x86_64-linux-gnu/bits/byteswap.h \
+ /usr/include/x86_64-linux-gnu/bits/uintn-identity.h \
+ /usr/include/x86_64-linux-gnu/sys/select.h \
+ /usr/include/x86_64-linux-gnu/bits/select.h \
+ /usr/include/x86_64-linux-gnu/bits/types/sigset_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__sigset_t.h \
+ /usr/include/alloca.h /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \
+ /usr/include/c++/9/bits/std_abs.h /usr/include/c++/9/cstdio \
+ /usr/include/stdio.h /usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/__fpos64_t.h \
+ /usr/include/x86_64-linux-gnu/bits/types/struct_FILE.h \
+ /usr/include/x86_64-linux-gnu/bits/types/cookie_io_functions_t.h \
+ /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
+ /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
+ /usr/include/c++/9/cerrno /usr/include/errno.h \
+ /usr/include/x86_64-linux-gnu/bits/errno.h /usr/include/linux/errno.h \
+ /usr/include/x86_64-linux-gnu/asm/errno.h \
/usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/functional_hash.h \
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- /broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/stdlib.h
+ /usr/include/x86_64-linux-gnu/bits/types/error_t.h \
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+ /usr/include/c++/9/bits/erase_if.h /usr/include/c++/9/stdlib.h
/usr/include/stdc-predef.h:
argProcessor.hpp:
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+/usr/include/c++/9/typeinfo:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/nested_exception.h:
+/usr/include/c++/9/bits/hash_bytes.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/memoryfwd.h:
+/usr/include/c++/9/bits/nested_exception.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_function.h:
+/usr/include/c++/9/bits/memoryfwd.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/backward/binders.h:
+/usr/include/c++/9/bits/stl_function.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/alloc_traits.h:
+/usr/include/c++/9/backward/binders.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/alloc_traits.h:
+/usr/include/c++/9/ext/alloc_traits.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/aligned_buffer.h:
+/usr/include/c++/9/bits/alloc_traits.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_map.h:
+/usr/include/c++/9/ext/aligned_buffer.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/initializer_list:
+/usr/include/c++/9/bits/stl_map.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/tuple:
+/usr/include/c++/9/initializer_list:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/utility:
+/usr/include/c++/9/tuple:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_relops.h:
+/usr/include/c++/9/utility:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/array:
+/usr/include/c++/9/bits/stl_relops.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/stdexcept:
+/usr/include/c++/9/array:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/string:
+/usr/include/c++/9/stdexcept:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stringfwd.h:
+/usr/include/c++/9/string:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/char_traits.h:
+/usr/include/c++/9/bits/stringfwd.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/postypes.h:
+/usr/include/c++/9/bits/char_traits.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cwchar:
+/usr/include/c++/9/bits/postypes.h:
+
+/usr/include/c++/9/cwchar:
/usr/include/wchar.h:
-/usr/include/stdio.h:
+/usr/include/x86_64-linux-gnu/bits/libc-header-start.h:
+
+/usr/include/x86_64-linux-gnu/bits/floatn.h:
+
+/usr/include/x86_64-linux-gnu/bits/floatn-common.h:
+
+/usr/lib/gcc/x86_64-linux-gnu/9/include/stdarg.h:
+
+/usr/include/x86_64-linux-gnu/bits/wchar.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/lib/gcc/x86_64-redhat-linux/7.3.0/include/stdarg.h:
+/usr/include/x86_64-linux-gnu/bits/types/wint_t.h:
-/usr/include/bits/wchar.h:
+/usr/include/x86_64-linux-gnu/bits/types/mbstate_t.h:
-/usr/include/xlocale.h:
+/usr/include/x86_64-linux-gnu/bits/types/__mbstate_t.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cstdint:
+/usr/include/x86_64-linux-gnu/bits/types/__FILE.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/lib/gcc/x86_64-redhat-linux/7.3.0/include/stdint.h:
+/usr/include/x86_64-linux-gnu/bits/types/FILE.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/locale_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/__locale_t.h:
+
+/usr/include/c++/9/cstdint:
+
+/usr/lib/gcc/x86_64-linux-gnu/9/include/stdint.h:
/usr/include/stdint.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/localefwd.h:
+/usr/include/x86_64-linux-gnu/bits/types.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/c++locale.h:
+/usr/include/x86_64-linux-gnu/bits/timesize.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/clocale:
+/usr/include/x86_64-linux-gnu/bits/typesizes.h:
-/usr/include/locale.h:
+/usr/include/x86_64-linux-gnu/bits/time64.h:
-/usr/include/bits/locale.h:
+/usr/include/x86_64-linux-gnu/bits/stdint-intn.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/iosfwd:
+/usr/include/x86_64-linux-gnu/bits/stdint-uintn.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cctype:
+/usr/include/c++/9/bits/localefwd.h:
-/usr/include/ctype.h:
+/usr/include/x86_64-linux-gnu/c++/9/bits/c++locale.h:
-/usr/include/bits/types.h:
+/usr/include/c++/9/clocale:
-/usr/include/bits/typesizes.h:
+/usr/include/locale.h:
-/usr/include/endian.h:
+/usr/include/x86_64-linux-gnu/bits/locale.h:
+
+/usr/include/c++/9/iosfwd:
+
+/usr/include/c++/9/cctype:
-/usr/include/bits/endian.h:
+/usr/include/ctype.h:
-/usr/include/bits/byteswap.h:
+/usr/include/x86_64-linux-gnu/bits/endian.h:
-/usr/include/bits/byteswap-16.h:
+/usr/include/x86_64-linux-gnu/bits/endianness.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/ostream_insert.h:
+/usr/include/c++/9/bits/ostream_insert.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/cxxabi_forced.h:
+/usr/include/c++/9/bits/cxxabi_forced.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/range_access.h:
+/usr/include/c++/9/bits/range_access.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/basic_string.h:
+/usr/include/c++/9/bits/basic_string.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/atomicity.h:
+/usr/include/c++/9/ext/atomicity.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/gthr.h:
+/usr/include/x86_64-linux-gnu/c++/9/bits/gthr.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/gthr-default.h:
+/usr/include/x86_64-linux-gnu/c++/9/bits/gthr-default.h:
/usr/include/pthread.h:
/usr/include/sched.h:
+/usr/include/x86_64-linux-gnu/bits/types/time_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/struct_timespec.h:
+
+/usr/include/x86_64-linux-gnu/bits/sched.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/struct_sched_param.h:
+
+/usr/include/x86_64-linux-gnu/bits/cpu-set.h:
+
/usr/include/time.h:
-/usr/include/bits/sched.h:
+/usr/include/x86_64-linux-gnu/bits/time.h:
+
+/usr/include/x86_64-linux-gnu/bits/timex.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/struct_timeval.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/clock_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/struct_tm.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/clockid_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/timer_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/struct_itimerspec.h:
+
+/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:
+
+/usr/include/x86_64-linux-gnu/bits/thread-shared-types.h:
-/usr/include/bits/time.h:
+/usr/include/x86_64-linux-gnu/bits/pthreadtypes-arch.h:
-/usr/include/bits/timex.h:
+/usr/include/x86_64-linux-gnu/bits/struct_mutex.h:
-/usr/include/bits/pthreadtypes.h:
+/usr/include/x86_64-linux-gnu/bits/struct_rwlock.h:
-/usr/include/bits/setjmp.h:
+/usr/include/x86_64-linux-gnu/bits/setjmp.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/x86_64-redhat-linux/bits/atomic_word.h:
+/usr/include/x86_64-linux-gnu/c++/9/bits/atomic_word.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/ext/string_conversions.h:
+/usr/include/c++/9/ext/string_conversions.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cstdlib:
+/usr/include/c++/9/cstdlib:
/usr/include/stdlib.h:
-/usr/include/bits/waitflags.h:
+/usr/include/x86_64-linux-gnu/bits/waitflags.h:
-/usr/include/bits/waitstatus.h:
+/usr/include/x86_64-linux-gnu/bits/waitstatus.h:
-/usr/include/sys/types.h:
+/usr/include/x86_64-linux-gnu/sys/types.h:
-/usr/include/sys/select.h:
+/usr/include/endian.h:
+
+/usr/include/x86_64-linux-gnu/bits/byteswap.h:
+
+/usr/include/x86_64-linux-gnu/bits/uintn-identity.h:
-/usr/include/bits/select.h:
+/usr/include/x86_64-linux-gnu/sys/select.h:
-/usr/include/bits/sigset.h:
+/usr/include/x86_64-linux-gnu/bits/select.h:
-/usr/include/sys/sysmacros.h:
+/usr/include/x86_64-linux-gnu/bits/types/sigset_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/__sigset_t.h:
/usr/include/alloca.h:
-/usr/include/bits/stdlib-float.h:
+/usr/include/x86_64-linux-gnu/bits/stdlib-float.h:
+
+/usr/include/c++/9/bits/std_abs.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/std_abs.h:
+/usr/include/c++/9/cstdio:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cstdio:
+/usr/include/stdio.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h:
+
+/usr/include/x86_64-linux-gnu/bits/types/__fpos64_t.h:
-/usr/include/libio.h:
+/usr/include/x86_64-linux-gnu/bits/types/struct_FILE.h:
-/usr/include/_G_config.h:
+/usr/include/x86_64-linux-gnu/bits/types/cookie_io_functions_t.h:
-/usr/include/bits/stdio_lim.h:
+/usr/include/x86_64-linux-gnu/bits/stdio_lim.h:
-/usr/include/bits/sys_errlist.h:
+/usr/include/x86_64-linux-gnu/bits/sys_errlist.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/cerrno:
+/usr/include/c++/9/cerrno:
/usr/include/errno.h:
-/usr/include/bits/errno.h:
+/usr/include/x86_64-linux-gnu/bits/errno.h:
/usr/include/linux/errno.h:
-/usr/include/asm/errno.h:
+/usr/include/x86_64-linux-gnu/asm/errno.h:
/usr/include/asm-generic/errno.h:
/usr/include/asm-generic/errno-base.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/functional_hash.h:
+/usr/include/x86_64-linux-gnu/bits/types/error_t.h:
+
+/usr/include/c++/9/bits/functional_hash.h:
+
+/usr/include/c++/9/bits/basic_string.tcc:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/basic_string.tcc:
+/usr/include/c++/9/bits/uses_allocator.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/uses_allocator.h:
+/usr/include/c++/9/bits/invoke.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/invoke.h:
+/usr/include/c++/9/bits/stl_multimap.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/bits/stl_multimap.h:
+/usr/include/c++/9/bits/erase_if.h:
-/broad/software/free/Linux/redhat_7_x86_64/pkgs/gcc_7.3.0/include/c++/7.3.0/stdlib.h:
+/usr/include/c++/9/stdlib.h:
=====================================
trinity-plugins/ParaFly/src/Makefile
=====================================
@@ -62,12 +62,12 @@ DIST_SOURCES = $(ParaFly_SOURCES)
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run aclocal-1.11
-AMTAR = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run tar
+ACLOCAL = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run tar
AM_CXXFLAGS = -pedantic -Wall -Wextra -Wno-long-long -Wno-deprecated -m64
-AUTOCONF = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoconf
-AUTOHEADER = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run autoheader
-AUTOMAKE = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run automake-1.11
+AUTOCONF = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run automake-1.11
AWK = gawk
CPPFLAGS =
CXX = g++
@@ -89,7 +89,7 @@ LDFLAGS =
LIBOBJS =
LIBS =
LTLIBOBJS =
-MAKEINFO = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/missing --run makeinfo
+MAKEINFO = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/missing --run makeinfo
MKDIR_P = /usr/bin/mkdir -p
OBJEXT = o
PACKAGE = parafly
@@ -100,13 +100,13 @@ PACKAGE_TARNAME = parafly
PACKAGE_VERSION = 0.1
PATH_SEPARATOR = :
SET_MAKE =
-SHELL = /bin/sh
+SHELL = /bin/bash
STRIP =
VERSION = 0.1
-abs_builddir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/src
-abs_srcdir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/src
-abs_top_builddir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
-abs_top_srcdir = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
+abs_builddir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/src
+abs_srcdir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/src
+abs_top_builddir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
+abs_top_srcdir = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
ac_ct_CXX =
am__include = include
am__leading_dot = .
@@ -125,7 +125,7 @@ host_alias =
htmldir = ${docdir}
includedir = ${prefix}/include
infodir = ${datarootdir}/info
-install_sh = ${SHELL} /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly/install-sh
+install_sh = ${SHELL} /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localedir = ${datarootdir}/locale
@@ -134,7 +134,7 @@ mandir = ${datarootdir}/man
mkdir_p = /usr/bin/mkdir -p
oldincludedir = /usr/include
pdfdir = ${docdir}
-prefix = /broad/hptmp/bhaas/trinityrnaseq-v2.15.1/trinity-plugins/ParaFly
+prefix = /home/bhaas/GITHUB/trinityrnaseq/trinity-plugins/ParaFly
program_transform_name = s,x,x,
psdir = ${docdir}
sbindir = ${exec_prefix}/sbin
=====================================
trinity-plugins/bamsifter/.gitmodules
=====================================
@@ -0,0 +1,4 @@
+[submodule "htslib"]
+ path = htslib
+ url = https://github.com/samtools/htslib.git
+ branch = master
=====================================
trinity-plugins/bamsifter/build_htslib.sh
=====================================
@@ -2,12 +2,11 @@
set -e -v
-tar xvf htslib-1.16.tar.bz2
-mv htslib-1.16 htslib
cd htslib
+git submodule init && git submodule update
mkdir -p build
-#autoheader
-#autoconf
+autoheader
+autoconf
./configure --prefix=`pwd`/build/
make
make install
=====================================
trinity-plugins/bamsifter/htslib-1.16.tar.bz2 deleted
=====================================
Binary files a/trinity-plugins/bamsifter/htslib-1.16.tar.bz2 and /dev/null differ
=====================================
trinity-plugins/bamsifter/sift_bam_max_cov.cpp
=====================================
@@ -4,6 +4,7 @@
#include <stdlib.h>
#include <string.h>
#include <cstring>
+#include <string>
#include <getopt.h>
#include <stdint.h>
#include <limits.h>
@@ -11,6 +12,7 @@
#include <set>
#include <utility>
#include <vector>
+#include <string>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
=====================================
util/align_and_estimate_abundance.pl
=====================================
@@ -326,11 +326,12 @@ unless ($est_method =~ /^(RSEM|kallisto|salmon|none)$/i) {
my @samples_to_process;
if ($samples_file) {
@samples_to_process = &parse_samples_file($samples_file);
- if ($samples_idx >= 0) {
+ if ($samples_idx > 0) {
my $num_samples = scalar(@samples_to_process);
if ($samples_idx > $num_samples) {
die "Error, sample index $samples_idx > $num_samples num samples ";
}
+ @samples_to_process = ($samples_to_process[$samples_idx-1]); # run only that sample
}
}
elsif ( ($left && $right) || $single) {
@@ -343,7 +344,6 @@ elsif ( ($left && $right) || $single) {
}
-
my $PE_mode = 1;
if ($single || (@samples_to_process && $samples_to_process[0]->{single})) {
=====================================
util/insilico_read_normalization.pl
=====================================
@@ -310,13 +310,13 @@ main: {
($left_SS_type, $right_SS_type) = split(//, $SS_lib_type);
}
- print STDERR "Converting input files. (both directions in parallel)";
+ print STDERR "Converting input files. (both directions in parallel);";
my $thr1;
my $thr2;
if (-s "left.fa" && -e "left.fa.ok") {
- $thr1 = threads->create(sub { print STDERR ("left file exists, nothing to do");});
+ $thr1 = threads->create(sub { print STDERR (" Left file exists, nothing to do;");});
}
else {
$thr1 = threads->create('prep_list_of_seqs', \@left_files, $seqType, "left", $left_SS_type);
@@ -324,7 +324,7 @@ main: {
}
if (-s "right.fa" && -e "right.fa.ok") {
- $thr2 = threads->create(sub { print STDERR ("right file exists, nothing to do");});
+ $thr2 = threads->create(sub { print STDERR (" Right file exists, nothing to do;");});
}
else {
$thr2 = threads->create('prep_list_of_seqs', \@right_files, $seqType, "right", $right_SS_type);
@@ -340,7 +340,7 @@ main: {
&process_checkpoints(@checkpoints);
- print STDERR "Done converting input files.";
+ print STDERR " Done converting input files. ";
push (@files_need_stats,
[\@left_files, "left.fa"],
@@ -426,7 +426,7 @@ main: {
foreach my $thread (@threads) {
$thread->join();
if ($thread->error()) {
- print STDERR "Error encountered with thread.\n";
+ print STDERR " Error encountered with thread.\n";
$num_fail++;
}
}
=====================================
util/misc/fastq_stats.pl
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
# written by
#
=====================================
util/misc/plot_ExN50_statistic.Rscript
=====================================
@@ -33,7 +33,7 @@ if (length(args) == 1) {
}
pdf(pdf_filename)
-p = alldata %>% ggplot(aes(x=Ex, y=ExN50, color=sample)) + geom_line() + xlim(c(30,100))
+p = alldata %>% filter(Ex >= 30) %>% ggplot(aes(x=Ex, y=ExN50, color=sample)) + geom_line() + xlim(c(30,100))
plot(p)
=====================================
util/misc/process_minimap2_alignments.pl
=====================================
@@ -27,6 +27,11 @@ my $usage = <<__EOUSAGE__;
# -I|--max_intron_length <int> maximum intron length (default: 100000)
#
# --incl_out_gff3 include gff3 formatted output file for alignments.
+# --allow_secondary allow secondary alignments (default secondary=no)
+#
+# --eqx include --eqx flag
+# --cs include long format via --cs w/ minimap2
+# --hq pacbio CCS reads (--splice:hq for mm2)
#
#######################################################################
@@ -44,7 +49,10 @@ my $help_flag;
my $output;
my $max_intron_length = 100000;
my $incl_out_gff3;
-
+my $allow_secondary = 0;
+my $include_cs_flag = 0;
+my $include_eqx_flag = 0;
+my $include_hq_flag = 0;
&GetOptions( 'h' => \$help_flag,
'genome=s' => \$genome,
@@ -54,6 +62,9 @@ my $incl_out_gff3;
'o|output=s' => \$output,
'I|max_intron_length=i' => \$max_intron_length,
'incl_out_gff3' => \$incl_out_gff3,
+ 'allow_secondary' => \$allow_secondary,
+ 'cs' => \$include_cs_flag,
+ 'hq' => \$include_hq_flag,
);
@@ -66,53 +77,71 @@ unless ($genome && $transcripts) {
die $usage;
}
+
+my $include_cs_param = "";
+my $include_cs_token = "";
+if ($include_cs_flag) {
+ $include_cs_param = "--cs";
+ $include_cs_token = ".cs";
+}
+
+my $include_eqx_param = "";
+my $include_eqx_token = "";
+if ($include_eqx_flag) {
+ $include_eqx_param = "--eqx";
+ $include_eqx_token = ".eqx";
+}
+
+
+my $include_hq_param = "";
+my $include_hq_token = "";
+if ($include_hq_flag) {
+ $include_hq_param = ":hq";
+ $include_hq_token = ".hq";
+}
+
+
unless ($output) {
- $output = basename($transcripts) . ".mm2.bam";
+ $output = basename($transcripts) . ".mm2${include_cs_token}${include_eqx_token}${include_hq_token}.bam";
}
+
+
+
main: {
- my $genomeBaseDir = dirname($genome);
- my $genomeName = basename($genome);
- my $genomeDir = "$genomeBaseDir/$genomeName" . ".mm2";
+ my $genomeBaseDir = dirname($genome);
+ my $genomeName = basename($genome);
+ my $mm2_idx = "$genomeBaseDir/$genomeName" . ".mm2";
+ my $cwd = cwd();
- unless (-d $genomeDir) {
- &process_cmd("mkdir $genomeDir");
- }
-
- my $cwd = cwd();
-
- my $mm2_idx = "$genomeDir/$genomeName.mmi";
-
- my $splice_file = "";
- if ($gtf) {
- $splice_file = "$genomeDir/anno.bed";
- }
-
+ my $splice_file = "$mm2_idx.splice.bed";
unless (-e $mm2_idx) {
my $cmd = "minimap2 -d $mm2_idx $genome";
&process_cmd($cmd);
-
- if ($gtf) {
- my $cmd = "paftools.js gff2bed $gtf > $splice_file";
- &process_cmd($cmd);
- }
-
}
+
+ if ($gtf && ! -s $splice_file) {
+ my $cmd = "paftools.js gff2bed $gtf > $splice_file";
+ &process_cmd($cmd);
+ }
+
- ## run minimap2
+ ## run minimap2
my $splice_param = "";
if ($splice_file) {
$splice_param = "--junc-bed $splice_file";
}
- my $cmd = "minimap2 -ax splice $splice_param --secondary=no -O6,24 -B4 -L -t $CPU -cs -ub -G $max_intron_length $mm2_idx $transcripts > $output.tmp.sam";
+ my $secondary = ($allow_secondary) ? "" : "--secondary=no";
+
+ my $cmd = "minimap2 --sam-hit-only -ax splice$include_hq_param $splice_param $secondary -t $CPU -u b -G $max_intron_length $include_cs_param $include_eqx_param $mm2_idx $transcripts > $output.tmp.sam";
&process_cmd($cmd);
$cmd = "samtools view -Sb -T $genome $output.tmp.sam -o $output.tmp.unsorted.bam";
@@ -130,8 +159,6 @@ main: {
&process_cmd($cmd);
}
-
-
unlink("$output.tmp.sam", "$output.tmp.unsorted.bam");
exit(0);
=====================================
util/misc/run_STAR_via_samples_file.pl
=====================================
@@ -164,7 +164,7 @@ main: {
. " --outSAMunmapped Within "
. " --limitBAMsortRAM=20000000000"
. " --limitOutSJcollapsed=10000000"
- . " --limitIObufferSize=300000000"
+ . " --limitIObufferSize=150000000 300000000"
. " --limitSjdbInsertNsj=10000000 "
;
@@ -187,8 +187,13 @@ main: {
$pipeliner->add_commands( new Command("samtools index $renamed_bam_outfile", "$checkpoint_dir/$renamed_bam_outfile.bai.ok") );
}
+ $pipeliner->add_commands( new Command("mv Log.final.out $sample_id.STAR.Log.final.out", "$checkpoint_dir/$sample_id.STAR_log_renamed.ok"));
+
$pipeliner->run();
+
+
+
}
=====================================
util/misc/try_estimate_TPM_filtering_threshold.Rscript
=====================================
@@ -26,7 +26,10 @@ main = function () {
data = read.table(gzfile(E_inputs_filename), header=T, com='', sep="\t", stringsAsFactors = F)
} else {
data = read.table(E_inputs_filename, header=T, com='', sep="\t", stringsAsFactors = F)
- }
+ }
+
+ orig_data = data
+
data = data %>% filter(max_expr_over_samples > 0.05 & max_expr_over_samples <= 2^5) # must have some evidence of expression
@@ -104,8 +107,8 @@ main = function () {
# compute some stats based on that threshold
- filtered_data = data %>% filter(max_expr_over_samples >= tpm_x) %>% arrange(desc(length))
- sum_length = sum(filtered_data$length)
+ filtered_data = orig_data %>% filter(max_expr_over_samples >= tpm_x) %>% arrange(desc(length))
+ sum_length = sum(filtered_data$length)
filtered_data = filtered_data %>% mutate(cumsum_len = cumsum(length))
half_length = sum_length / 2
N50_entry = filtered_data %>% filter(cumsum_len <= half_length) %>% filter(row_number() == n())
=====================================
util/support_scripts/run_UpperQuartileNormalization_matrix.Rscript
=====================================
@@ -0,0 +1,35 @@
+#!/usr/bin/env Rscript
+
+################################################
+# for info on upper quartile normalization, see:
+# http://vinaykmittal.blogspot.com/2013/10/fpkmrpkm-normalization-caveat-and-upper.html
+################################################
+
+suppressPackageStartupMessages(library("argparse"))
+
+parser = ArgumentParser()
+parser$add_argument("--matrix", help="input data file", required=TRUE, nargs=1)
+parser$add_argument("--output", help="output data file", required=TRUE, nargs=1)
+
+args = parser$parse_args()
+matrix_filename = args$matrix
+output_filename = args$output
+
+data = read.table(gzfile(matrix_filename), header=T, sep="\t", row.names=1, check.names=F, com='')
+
+
+get_upper_quartile = function(vec) {
+ vec = vec[vec > 0]
+ quantile(vec, 0.75)
+}
+
+data = as.matrix(data)
+upp_quartiles = apply(data, 2, get_upper_quartile)
+m = sweep(data, MARGIN=2, upp_quartiles, '/')
+mean_upp_quart = mean(upp_quartiles)
+m = m * mean_upp_quart
+write.table(m, file=output_filename, quote=F, sep="\t", col.names=NA)
+
+
+quit(save = "no", status = 0, runLast = FALSE)
+
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/commit/ae0404ed6db07b2fd3d8f3d4e06d0a6e40b6f598
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/commit/ae0404ed6db07b2fd3d8f3d4e06d0a6e40b6f598
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