default: all

#include $(MAKEFILES_DIR)/Sentinel.mk

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT1_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT1_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --target=check) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/EXP_LANE_SPLIT_1_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/EXP_LANE_SPLIT_1_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --exportSet=1 --read1Export=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Aligned/Project_Demo/Sample_PhiX/PhiX_TTAGGC_L001_R1_001_export.txt.gz --read2Export=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Aligned/Project_Demo/Sample_PhiX/PhiX_TTAGGC_L001_R2_001_export.txt.gz --target=split) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/EXP_LANE_SPLIT_1_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT1_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT2_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT2_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/EXP_LANE_SPLIT_1_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT3_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT3_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --target=commit) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT3_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT2_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT5_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT5_N0.finished.done: 

tmp/make/tasks_2011-10-18_22-47-12.txt/phix_0000_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/phix_0000_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/splitUnSorted.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom='phix' --binId=0000 --target=split) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/phix_0000_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT3_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/phix_0000_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNC_RM_SPLIT_TEMP_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNC_RM_SPLIT_TEMP_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/sortExport.pl --projectDir='/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX' --target=removeTemps) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNC_RM_SPLIT_TEMP_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_DUPL2_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_DUPL2_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateStats.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --target=duplicates) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_DUPL2_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateReports.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --target=duplicates) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_DUPL2_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/buildphix_0000_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/buildphix_0000_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/splitUnSorted.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom='phix' --binId=0000 --target=merge) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/buildphix_0000_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_phix_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_phix_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/buildphix_0000_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/SORTED2BAM_phix_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SORTED2BAM_phix_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/concatChromBam.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom=phix) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SORTED2BAM_phix_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_phix_DONE_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_phix_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_phix_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SORTED2BAM_phix_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_phix_DONE_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N1.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N1.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/splitUnSorted.pl --projectDir='/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX' --target=removeTemps) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N1.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_BAM_DONE_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N1.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_phix_DONE_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_refSeq_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_refSeq_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT1_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/transformFasta.pl --chromNameSource=contigName --targetPath=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX/cachedRefSeq /illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa && /illumina/development/casava/Version_1_8_branch/bin/configureBuild.pl --chromNameSource=fileName --refSequences=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX/cachedRefSeq --maskRefSeqFiles='*' --outDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --targets continue) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_refSeq_DONE_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/refSeq_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/refSeq_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_INDEL_FINDER_phix_0000_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_INDEL_FINDER_phix_0000_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/refSeq_DONE_N0.finished.done tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_phix_DONE_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_0000_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_0000_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/runGrouperBin.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom=phix --binId=0000) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_0000_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_INDEL_FINDER_phix_0000_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_0000_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_VARIANTS_phix_0000_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_VARIANTS_phix_0000_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/refSeq_DONE_N0.finished.done tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_phix_DONE_N0.finished.done tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_phix_0000_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_0000_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_0000_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/callSmallVariants.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom='phix' --binId=0000) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_0000_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/PREREQ_VARIANTS_phix_0000_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_0000_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_FILTER_phix_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_FILTER_phix_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/filterSmallVariants.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --chrom='phix') >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_FILTER_phix_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_phix_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_FILTER_phix_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_STATS_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_STATS_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateVariantsStats.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_STATS_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N1.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N1.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2/generateVariantsReports.pl --projectDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N1.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/VARIANTS_STATS_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N1.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N0.finished

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/refSeqClean_PREREQ_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/refSeqClean_PREREQ_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_EXPORT5_N0.finished.done tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_SORT2_N1.finished tmp/make/tasks_2011-10-18_22-47-12.txt/INDEL_FINDER_N0.finished.done tmp/make/tasks_2011-10-18_22-47-12.txt/REPORT_N1.finished tmp/make/tasks_2011-10-18_22-47-12.txt/SYNCH_MERGE_DONE_N0.finished.done

tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_CLEANUP_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_CLEANUP_N0.finished).sentinel
	(/illumina/development/casava/Version_1_8_branch/bin/configureBuild.pl --outDir=/illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX --targets continue --chromNameSource=contigName --refSequences=/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2/examples/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes --maskRefSeqFiles=phix.fa && rm -rf /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX/cachedRefSeq ) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_CLEANUP_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/refSeqClean_PREREQ_N0.finished.done

.SECONDARY: tmp/make/tasks_2011-10-18_22-47-12.txt/ALL_DONE_N0.finished.done
tmp/make/tasks_2011-10-18_22-47-12.txt/ALL_DONE_N0.finished.done: tmp/make/tasks_2011-10-18_22-47-12.txt/SPLIT_REF_SEQ_CLEANUP_N0.finished

tmp/make/tasks_2011-10-18_22-47-12.txt/postRunCmd_N0.finished: $(dir tmp/make/tasks_2011-10-18_22-47-12.txt/postRunCmd_N0.finished).sentinel
	(cd /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX && CASAVA_FULL_ETCDIR="/illumina/development/casava/Version_1_8_branch/etc/CASAVA-1.8.2" CASAVA_FULL_DATADIR="/illumina/development/casava/Version_1_8_branch/share/CASAVA-1.8.2" CASAVA_FULL_BINDIR="/illumina/development/casava/Version_1_8_branch/bin" CASAVA_FULL_LIBDIR="/illumina/development/casava/Version_1_8_branch/lib/CASAVA-1.8.2" CASAVA_FULL_LIBEXECDIR="/illumina/development/casava/Version_1_8_branch/libexec/CASAVA-1.8.2" CASAVA_FULL_PERL_LIBDIR="/illumina/development/casava/Version_1_8_branch/lib/CASAVA-1.8.2/perl"  touch /illumina/development/casava/Version_1_8_branch/bin/ValidationMultiplexed/Build/Project_Demo/Sample_PhiX/Build.finished) >&2 \
    $(AND) $(TOUCH) $@

tmp/make/tasks_2011-10-18_22-47-12.txt/postRunCmd_N0.finished: tmp/make/tasks_2011-10-18_22-47-12.txt/ALL_DONE_N0.finished.done

all: tmp/make/tasks_2011-10-18_22-47-12.txt/postRunCmd_N0.finished