1 EXPTRACK_DIR=$(HTSW_ANALYSIS_ROOT)
4 FLOWCELL=$(shell pwd | awk -F/ '{print $$NF}')
5 FILES=$(shell ls -1d *.align*.txt)
6 QPCR_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.qPCR/)
7 COUNT_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.count/)
8 PROFILE_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.profile/)
9 PROFILE_IMAGES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.profile.png/)
10 PERCENT_BASE_IMAGES=$(shell ls -1d *.pf.txt.gz | sed -e s/pf.txt.gz/percent_base.png/)
12 all: $(QPCR_FILES) $(PROFILE_FILES) $(PROFILE_IMAGES) $(PERCENT_BASE_IMAGES) $(COUNT_FILES) $(FILES) $(FLOWCELL)_qPCR_summary.txt $(FLOWCELL)_qPCR_summary.html $(FLOWCELL)_LibraryInfo.xml $(FLOWCELL)_SequencingSummary.html $(FLOWCELL)_QC_Summary.html
15 grep -v contam $< | awk '{if(NF > 3) {print $$1} }' | wc -l > $@;
18 echo $(EXPTRACK_DIR)/bin/qPCR $< $(EXPTRACK_DIR)/reference_data/GenericBackground $(EXPTRACK_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r | awk -F\/ '{print $$NF}'
19 $(EXPTRACK_DIR)/bin/qPCR $< $(EXPTRACK_DIR)/reference_data/GenericBackground $(EXPTRACK_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r | awk -F\/ '{print $$NF}' > $@
22 $(EXPTRACK_DIR)/bin/profile_reads_against_features $< $(EXPTRACK_DIR)/reference_data/`basename $< | awk -F\. '{ print $$3 }'`_tx_start_sites > $@
24 %.txt.profile.png: %.txt.profile
25 cat $(EXPTRACK_DIR)/conf/TSSProfileFormat.gnuplot | sed -e s#FILENAME#$<#g -e s#OUTNAME#$@# | gnuplot;
27 # new software to profile base composition .
28 %.percent_base: %.pf.txt.gz
29 cat $< | gzip -d | $(EXPTRACK_DIR)/scripts/count_bases.pm > $@
31 %.percent_base.png: %.percent_base
32 cat $(EXPTRACK_DIR)/conf/PercentBaseFormat.gnuplot | sed -e s#FILENAME#$<#g -e s#OUTNAME#$@# | gnuplot;
34 $(FLOWCELL)_qPCR_summary.txt: $(QPCR_FILES)
36 for f in $^; do echo `echo $$f` `cat $$f | head -n 1` >> $@; echo `echo $$f` `cat $$f | head -n 2 | tail -n 1` >> $@; done;
38 $(FLOWCELL)_qPCR_summary.html: $(FLOWCELL)_qPCR_summary.txt;
39 cat $< | $(EXPTRACK_DIR)/scripts/QC_Summarize_qPCR.pm > $@
41 $(FLOWCELL)_LibraryInfo.xml: $(COUNT_FILES)
42 $(EXPTRACK_DIR)/scripts/CollectLibraries.pm `ls *.align*.txt` > $@
44 $(FLOWCELL)_SequencingSummary.html: $(FLOWCELL)_LibraryInfo.xml
45 $(EXPTRACK_DIR)/scripts/SummarizeLibrary.pm $< > $@
47 $(FLOWCELL)_QC_Summary.html: $(FLOWCELL)_SequencingSummary.html $(FLOWCELL)_qPCR_summary.html $(PROFILE_FILES)
48 $(EXPTRACK_DIR)/scripts/WriteQCSummary.pm $(FLOWCELL)_LibraryInfo.xml $(FLOWCELL)_qPCR_summary.txt > $@;