Major analysis server update. Had to switch to a new server, and used the opportunity...

[htsworkflow.git] / htswanalysis / scripts / Flowcell_QC_Makefile

diff --git a/htswanalysis/scripts/Flowcell_QC_Makefile b/htswanalysis/scripts/Flowcell_QC_Makefile
index fa3fd8bd322dd4abe9164bf53d2a43f04aa229fe..8f91e433a4fe9b836492fde10170e6a04ebdacb6 100644 (file)
--- a/htswanalysis/scripts/Flowcell_QC_Makefile
+++ b/htswanalysis/scripts/Flowcell_QC_Makefile
@@ -9,14 +9,14 @@ PROFILE_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.profile/)
 PROFILE_IMAGES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.profile.png/)
 PERCENT_BASE_IMAGES=$(shell ls -1d *.pf.txt.gz | sed -e s/pf.txt.gz/percent_base.png/)
 
-all: $(QPCR_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
+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
 
 %.txt.count: %.txt
        grep -v contam $< | awk '{if(NF > 3) {print $$1} }' | wc -l > $@;
 
 %.txt.qPCR: %.txt
-       echo $(EXPTRACK_DIR)/qPCR/qPCR $< $(EXPTRACK_DIR)/qPCR/GenericBackground $(EXPTRACK_DIR)/qPCR/Tests/ | sort -k 2 -g -r | sed -e "s#SolexaSoftware/qPCR/Tests//##"
-       $(EXPTRACK_DIR)/qPCR/qPCR $< $(EXPTRACK_DIR)/qPCR/GenericBackground $(EXPTRACK_DIR)/qPCR/Tests/ | sort -k 2 -g -r | sed -e "s#SolexaSoftware/qPCR/Tests//##" > $@
+       echo $(EXPTRACK_DIR)/bin/qPCR $< $(EXPTRACK_DIR)/reference_data/GenericBackground $(EXPTRACK_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r | awk -F\/ '{print $$NF}'
+       $(EXPTRACK_DIR)/bin/qPCR $< $(EXPTRACK_DIR)/reference_data/GenericBackground $(EXPTRACK_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r | awk -F\/ '{print $$NF}' > $@
 
 %.txt.profile: %.txt
        $(EXPTRACK_DIR)/bin/profile_reads_against_features $< $(EXPTRACK_DIR)/reference_data/`basename $< | awk -F\. '{ print $$3 }'`_tx_start_sites > $@