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include Mf.common
.SECONDARY:
.PHONY: all
all: real sims_run
#all: prep real sims_generate sims_run bench bench_memUsage
real:
$(MAKE) All_Gene_Real genome=human_CR_3.0.0 sample=10X/3/pbmc_5k threadRun=20/run1
$(MAKE) All_GeneFull_Real genome=human_CR_3.0.0 sample=10X/3/pbmc_5k threadRun=20/run1
sims_generate: # generates simulated data
$(MAKE) -C sims
sims_run:
$(MAKE) All_Gene_Sims genome=human_CR_3.0.0 sample=10X/3/pbmc_5k_sims_human_CR_3.0.0_MultiGeneNo threadRun=20/run1
$(MAKE) All_Gene_Sims genome=human_CR_3.0.0 sample=10X/3/pbmc_5k_sims_human_CR_3.0.0_MultiGeneYes threadRun=20/run1
$(MAKE) All_Gene_Sims genome=human_CR_3.0.0 sample=10X/3/pbmc_5k_sims_human_CR_3.0.0_MultiGeneNo_OnlyExonicReads threadRun=20/run1
bench:
$(MAKE) bench/All_Gene_Real benchThreadNumbers="20 8 12 4 16" genome=human_CR_3.0.0 sample=10X/3/pbmc_5k
$(MAKE) bench/All_GeneFull_Real benchThreadNumbers="20 8 12 4 16" genome=human_CR_3.0.0 sample=10X/3/pbmc_5k
bench_memUsage:
$(MAKE) bench/Gene/CellRanger benchThreadNumbers="20 16 12 8 4" benchRunIndexes="memUse1" genome=human_CR_3.0.0 sample=10X/3/pbmc_5k PREPoption="memUsage"
####################################################################################################################### extras
real_Gencode37:
$(MAKE) All_Gene_Real genome=h38_Gencode37 sample=10X/3/pbmc_5k threadRun=20/run1
real_mult:
$(MAKE) -f Mf.count count/STAR_2.7.9x/human_CR_3.0.0/fullSA/10X_CR4_noSAM_mult/10X/3/pbmc_5k/20/run1/CO
$(MAKE) -f Mf.count count/STAR_2.7.9x/human_CR_3.0.0/fullSA/10X_CR4_noSAM_mult_UniqueGenomic/10X/3/pbmc_5k/20/run1/CO
release_tests:
$(MAKE) -f Mf.count count/STAR_2.7.9a/human_CR_3.0.0/fullSA/10X_CR4_noSAM/10X/3/pbmc_5k/20/relTest/CO
$(MAKE) -f Mf.count count/STAR_2.7.9a/human_CR_3.0.0/fullSA/10X_CR4_noSAM_mult/10X/3/pbmc_5k/20/relTest/CO
$(MAKE) -f Mf.count count/STAR_2.7.9a/human_CR_3.0.0/fullSA/10X_noSAM_sims_mult_ENCODE/10X/3/pbmc_5k_sims_MultiGeneNo/20/relTest/CO
$(MAKE) -f Mf.count count/STAR_2.7.9a/human_CR_3.0.0/fullSA/10X_noSAM_sims_mult_ENCODE/10X/3/pbmc_5k_sims_MultiGeneYes/20/relTest/CO
real_TM_select5: samples=TM_10X_P7_0 TM_10X_P4_2 TM_10X_P7_9 TM_10X_P8_14 TM_10X_P7_6
real_TM_select5:
for s1 in $(samples); do \
$(MAKE) Gene_Real_Ssp-Afd-Ask-kb genome=mouse_CR_3.0.0 sample=10X/2/$$s1 threadRun=20/run1; \
done
sims_all_mouse:
$(MAKE) All_Gene_Sims genome=mm10_GencodeM21_Diane sample=10X/2/mouse_ENCSR642XVO_sims_mm10_GencodeM21_Diane_MultiGeneNo threadRun=20/run1
$(MAKE) All_Gene_Sims genome=mm10_GencodeM21_Diane sample=10X/2/mouse_ENCSR642XVO_sims_mm10_GencodeM21_Diane_MultiGeneYes threadRun=20/run1
$(MAKE) All_Gene_Sims genome=mm10_GencodeM21_Diane sample=10X/2/mouse_ENCSR642XVO_sims_mm10_GencodeM21_Diane_MultiGeneNo_OnlyExonicReads threadRun=20/run1
$(MAKE) All_Gene_Sims genome=mm10_GencodeM21_Diane sample=10X/2/mouse_ENCSR642XVO_sims_mm10_GencodeM21_Diane_MultiGeneYes_OnlyExonicReads threadRun=20/run1
############################################################ Versions
alevin-fry := salmon-alevin-fry_1.4.0_0.1.0
kbpy := kbpy_0.25.0
STAR := STAR_2.7.9a
CellRanger := CellRanger_5.0.1
############################################################ Bench
#benchThreadNumbers := 20 12 8 4 16
benchRunIndexes ?= b01 b02 b03 b04 b05
bench/%: benchOpts= PREPoption=sleep
bench/%:
for rr in $(benchRunIndexes); do \
for tt in $(benchThreadNumbers); do \
$(MAKE) $* threadRun=$$tt/$$rr genome=$(genome) sample=$(sample) $(benchOpts) ; \
done; \
done
#$(MAKE) $* threadRun=$$tt/$$rr genome=$(genome) sample=$(sample); \
############################################################ tools and options
# Gene: standard gene expression
All_GeneFull_Real: \
GeneFull/kbpy \
GeneFull/STAR_CR4 \
# GeneFull/CellRanger \
All_Gene_Sims: Gene/STAR_sims \
Gene/kbpy \
Gene/alevin-fry
All_Gene_Real: \
Gene/kbpy \
Gene/alevin-fry \
Gene/STAR_CR4 \
Gene/CellRanger
Gene_Real_Ssp-Afd-Ask-kb:
make -f Mf.count count/$(STAR)/$(genome)/sparseSA3/10X_CR4_noSAM/$(sample)/$(threadRun)/CO
make -f Mf.count count/$(kbpy)/$(genome)/standard_1/default/$(sample)/$(threadRun)/CO
make -f Mf.count count/$(alevin-fry)/$(genome)/standard/sketch_rad/$(sample)/$(threadRun)/CO afGplOpt=knee
make -f Mf.count count/$(alevin-fry)/$(genome)/decoyFull/rad/$(sample)/$(threadRun)/CO afGplOpt=knee
Gene/CellRanger:
make -f Mf.count count/$(CellRanger)/$(genome)/standard/default/$(sample)/$(threadRun)/CO
GeneFull/CellRanger:
make -f Mf.count count/$(CellRanger)/$(genome)/standard/intronic/$(sample)/$(threadRun)/CO
Gene/STAR_sims:
$(MAKE) -f Mf.count count/$(STAR)/$(genome)/fullSA/10X_noSAM_sims_mult_ENCODE/$(sample)/$(threadRun)/CO
Gene/STAR_CR4:
make -f Mf.count count/$(STAR)/$(genome)/fullSA/10X_CR4_noSAM/$(sample)/$(threadRun)/CO
make -f Mf.count count/$(STAR)/$(genome)/sparseSA3/10X_CR4_noSAM/$(sample)/$(threadRun)/CO
GeneFull/STAR_CR4:
$(MAKE) -f Mf.count count/$(STAR)/$(genome)/fullSA/10X_CR4_GeneFull_noSAM/$(sample)/$(threadRun)/CO
$(MAKE) -f Mf.count count/$(STAR)/$(genome)/sparseSA3/10X_CR4_GeneFull_noSAM/$(sample)/$(threadRun)/CO
Gene/kbpy:
make -f Mf.count count/$(kbpy)/$(genome)/standard_1/default/$(sample)/$(threadRun)/CO
make -f Mf.count count/$(kbpy)/$(genome)/standard_1/mult/$(sample)/$(threadRun)/CO
GeneFull/kbpy:
make -f Mf.count count/$(kbpy)/$(genome)/nucleus_1/default/$(sample)/$(threadRun)/CO
#make -f Mf.count count/$(kbpy)/$(genome)/nucleus_8/default/$(sample)/$(threadRun)/CO
#make -f Mf.count count/$(kbpy)/$(genome)/nucleus_2/default/$(sample)/$(threadRun)/CO
#make -f Mf.count count/$(kbpy)/$(genome)/nucleus_4/default/$(sample)/$(threadRun)/CO
Gene/alevin-fry:
make -f Mf.count count/$(alevin-fry)/$(genome)/standard/sketch_rad/$(sample)/$(threadRun)/CO afGplOpt=knee
make -f Mf.count count/$(alevin-fry)/$(genome)/standard/rad/$(sample)/$(threadRun)/CO afGplOpt=knee
make -f Mf.count count/$(alevin-fry)/$(genome)/decoyFull/rad/$(sample)/$(threadRun)/CO afGplOpt=knee
make -f Mf.count count/$(alevin-fry)/$(genome)/decoyPartial/rad/$(sample)/$(threadRun)/CO afGplOpt=knee
################################## Prep
.PHONY: prep samples exe genomes
prep: data samples exe genomes
data:
$(MAKE) -C data
samples:
$(MAKE) -C samples
exe:
$(MAKE) -C exe
genomes:
$(MAKE) -C genomes