From 9ed25df3e14e503469234f9f6c4c7d1283341662 Mon Sep 17 00:00:00 2001 From: Tim Reddy Tim Date: Thu, 28 Aug 2008 23:39:33 +0000 Subject: [PATCH] First complete Projects/Tasks build. --- htswanalysis/scripts/ConfigureTasks.pm | 9 +++++++-- htswanalysis/scripts/LibrariesMakefile | 20 ++++++++++---------- htswanalysis/scripts/SummarizeProject2.pm | 23 +++++++++++++---------- 3 files changed, 30 insertions(+), 22 deletions(-) diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm index bf7b5e0..ab5f785 100755 --- a/htswanalysis/scripts/ConfigureTasks.pm +++ b/htswanalysis/scripts/ConfigureTasks.pm @@ -21,6 +21,11 @@ my $root_dir = shift; my $data_dir = shift; my $parm = shift; +if(!defined($root_dir) || !defined($data_dir)) { + print "Usage: ./ConfigureTasks.pm [root_dir] [data_dir] {option} \n"; + exit(); +} + my %libs; my $BIOP = "$root_dir/bin/BioProspector.mac"; @@ -89,12 +94,12 @@ my $index_list = ""; for(split(/ /,$projects)) { $index_list .= "$_/index.html "; } open(MAKE,">$data_dir/Projects/ProjectMakefile"); -print MAKE "all: $index_list | .start\n\n.PHONY: $index_list .start\n\n.start:\n\ttouch .start; echo \"Projects updated at `date`\";\n\n$index_list:\n\t".'cd `dirname $@` && $SUMMARIZE_PROJECT ../../LibraryInfo.xml > `basename $@`'."\n"; +print MAKE "all: $index_list | .start\n\n.PHONY: $index_list .start\n\n.start:\n\ttouch .start; echo \"Projects updated at `date`\";\n\n$index_list:\n\t".'cd `dirname $@` && '.$SUMMARIZE_PROJECT.' '.$root_dir.' '.$data_dir.'/LibraryInfo.xml > `basename $@`'."\n"; close(MAKE); print STDERR "Project makefile compete. Starting to build tasks\n"; -`make -j 4 -f TaskMakefile > make_tasks.log 2> make_tasks.err`; +`cd $data_dir/Projects && make -j 4 -f TaskMakefile > make_tasks.log 2> make_tasks.err`; sub writeProject { my $project = shift; diff --git a/htswanalysis/scripts/LibrariesMakefile b/htswanalysis/scripts/LibrariesMakefile index ec29172..4a779dd 100644 --- a/htswanalysis/scripts/LibrariesMakefile +++ b/htswanalysis/scripts/LibrariesMakefile @@ -30,7 +30,7 @@ CMPLX_FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMa PROFILE_FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMakefile.err | sed -e s/txt/txt.profile/) LIBFILES=$(shell ls -1d $(DATA_DIR)/Libraries/.*.config 2>> LibrariesMakefile.err | sed -e s/config/txt/ -e "s/\/\./\//") -all: $(QPCR_FILES) $(COUNT_FILES) $(FILES) qPCR_summary.txt LibraryInfo.xml $(LIBFILES) SequencingSummary.html Distribute +all: $(QPCR_FILES) $(COUNT_FILES) $(FILES) $(DATA_DIR)/qPCR_summary.txt $(DATA_DIR)/LibraryInfo.xml $(LIBFILES) $(DATA_DIR)/SequencingSummary.html Distribute %.txt.complexity: %.txt $(ROOT_DIR)/bin/complexity_count `basename $<` $< > $@ @@ -48,17 +48,17 @@ all: $(QPCR_FILES) $(COUNT_FILES) $(FILES) qPCR_summary.txt LibraryInfo.xml $(LI $(DATA_DIR)/Libraries/%.txt: $(DATA_DIR)/Libraries/.%.config | LibraryInfo.xml cat `cat $<` > $@; -qPCR_summary.txt: $(QPCR_FILES) - rm -f qPCR_summary.txt; - for f in $^; do echo `echo $$f` `cat $$f | head -n 1` >> qPCR_summary.txt; done; - cat qPCR_summary.txt | sort -k 2,1 -g -r > t; mv t qPCR_summary.txt; +$(DATA_DIR)/qPCR_summary.txt: $(QPCR_FILES) + rm -f $@; + for f in $^; do echo `echo $$f` `cat $$f | head -n 1` >> $@; done; + cat $@ | sort -k 2,1 -g -r > t && mv t $@; -LibraryInfo.xml: $(COUNT_FILES) $(CMPLX_FILES) - $(ROOT_DIR)/scripts/CollectLibraries.pm $(DATA_DIR) > LibraryInfo.xml - $(ROOT_DIR)/scripts/RecompileLibraries.pm LibraryInfo.xml $(DATA_DIR) +$(DATA_DIR)/LibraryInfo.xml: $(COUNT_FILES) $(CMPLX_FILES) + $(ROOT_DIR)/scripts/CollectLibraries.pm $(DATA_DIR) > $@; + $(ROOT_DIR)/scripts/RecompileLibraries.pm $@ $(DATA_DIR) -SequencingSummary.html: LibraryInfo.xml - $(ROOT_DIR)/scripts/SummarizeLibrary.pm LibraryInfo.xml > SequencingSummary.html +$(DATA_DIR)/SequencingSummary.html: $(DATA_DIR)/LibraryInfo.xml + $(ROOT_DIR)/scripts/SummarizeLibrary.pm $< > $@; Distribute: SequencingSummary.html qPCR_summary.txt cp $^ $(HTML_DIR); diff --git a/htswanalysis/scripts/SummarizeProject2.pm b/htswanalysis/scripts/SummarizeProject2.pm index 470e0a9..546dd45 100755 --- a/htswanalysis/scripts/SummarizeProject2.pm +++ b/htswanalysis/scripts/SummarizeProject2.pm @@ -2,6 +2,7 @@ use strict; use warnings; use XML::Simple; +my $root_dir = shift; my $library_info = shift; my %libs; my %quest; @@ -27,17 +28,17 @@ for my $i (0..scalar(@{$xml->{PeakCalling}})-1) { $desc{outfile} = ""; $desc{fasta} = ""; if($caller eq "QuEST") { - $desc{Summary} = `~/EXPTRACK/ProjectScripts/SummarizeQuEST.pm $caller_dir`; + $desc{Summary} = `$root_dir/scripts/SummarizeQuEST.pm $caller_dir`; $desc{outfile} = "$caller_dir/peak_caller.ChIP.out.bedgraph"; $desc{fasta} = "$caller_dir/peak_caller.ChIP.out.fasta"; } elsif($caller eq "WingPeaks") { - $desc{Summary} = `~/EXPTRACK/ProjectScripts/SummarizeWingPeaks.pm $caller_dir/$name.peaks`; + $desc{Summary} = `$root_dir/scripts/SummarizeWingPeaks.pm $caller_dir/$name.peaks`; $desc{outfile} = "$caller_dir/$name.peaks.bed"; $desc{fasta} = "$caller_dir/$name.peaks.fasta"; } elsif($caller eq "MACS") { my $peakfile = $caller_dir.'/'.$name.'_peaks.xls'; my $negpeakfile = $caller_dir.'/'.$name.'_negative_peaks.xls'; - $desc{Summary} = `~/EXPTRACK/ProjectScripts/SummarizeMACS.pm $peakfile $negpeakfile`; + $desc{Summary} = `$root_dir/scripts/SummarizeMACS.pm $peakfile $negpeakfile`; $desc{outfile} = "$caller_dir/".$name."_peaks.bed"; $desc{fasta} = "$caller_dir/".$name."_peaks.fasta"; } @@ -62,7 +63,7 @@ for my $i (0..scalar(@{$xml->{qPCR}})-1) { $libs{$lib} = 0; if( ! -e $outfile ) { $qPCR_Summary .= "$nameProcessing...\n"; } else { - my $summary_line = `~/EXPTRACK/ProjectScripts/Summarize_qPCR.pm $name $lib $outfile`; + my $summary_line = `$root_dir/scripts/Summarize_qPCR.pm $name $lib $outfile`; if($summary_line eq "") { $qPCR_Summary .= "$nameProcessing...\n"; } else { $qPCR_Summary .= $summary_line; @@ -99,18 +100,20 @@ for my $i (0..scalar(@{$xml->{CompareLibraries}})-1) { my $task = $xml->{CompareLibraries}->[$i]->{TaskId}; my $tf = $xml->{CompareLibraries}->[$i]->{TF}; my $genome = $xml->{CompareLibraries}->[$i]->{Genome}; - my $features = "~/EXPTRACK/compare_peak_calls/".$genome."_uptream5k_downtream1k"; + my $features = "$root_dir/reference_data/".$genome."_uptream5k_downtream1k"; my $name1 = $xml->{CompareLibraries}->[$i]->{Library}->[0]->{Library}; my $name2 = $xml->{CompareLibraries}->[$i]->{Library}->[1]->{Library}; my $outfile = "../../Tasks/".$task.'/'.$name1."_".$name2.".compare"; $libs{$name1} = 0; $libs{$name2} = 0; my $correlation; - if(-e $outfile) { $correlation = `cat $outfile | awk '{print \$8}'`; } - my $color; if( !(-e $outfile) ) { $correlation = "In Progress..."; $color = "#FFBBBB"; } - elsif($correlation > 0.9) { $color = "#BBFFBB"; } - elsif($correlation > 0.6) { $color = "#BBBBFF"; } - else { $color = "#FFBBBB"; } + else { + if(-e $outfile) { $correlation = `cat $outfile | awk '{print \$8}'`; } + my $color; + elsif($correlation > 0.9) { $color = "#BBFFBB"; } + elsif($correlation > 0.6) { $color = "#BBBBFF"; } + else { $color = "#FFBBBB"; } + } $library_comparisons .= "$tf$name1$name2$correlation\n"; } $library_comparisons .= "\n"; -- 2.30.2