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Makefile
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ifneq ("$(wildcard config.inc)", "")
include config.inc
endif
ifneq ("$(wildcard project_config.inc)", "")
include project_config.inc
endif
include innovation-lab/config/config.inc
export
NUM_ATTEMPTS ?= 10
NOW := $(shell date +"%F")
MAKELOG = log/$(@).$(NOW).log
USE_CLUSTER ?= true
QMAKE = innovation-lab/dodo-cloning-kit/runtime/qmake.pl -n $@.$(NOW) $(if $(SLACK_CHANNEL),-c $(SLACK_CHANNEL)) -r $(NUM_ATTEMPTS) -m -s -- make
NUM_JOBS ?= 250
define RUN_QMAKE
$(QMAKE) -e -f $1 -j $2 $(TARGET) && \
mkdir -p completed_tasks && \
touch completed_tasks/$@
endef
RUN_MAKE = $(if $(findstring false,$(USE_CLUSTER))$(findstring n,$(MAKEFLAGS)),+$(MAKE) -f $1,$(call RUN_QMAKE,$1,$(NUM_JOBS)))
#==================================================
# MSK-ACCESS
#==================================================
TARGETS += fgbio_access
fgbio_access :
$(call RUN_MAKE,innovation-lab/msk_access/fgbio_access.mk)
TARGETS += genotype_access
genotype_access :
$(call RUN_MAKE,innovation-lab/msk_access/genotype_access.mk)
TARGETS += cluster_access
cluster_access :
$(call RUN_MAKE,innovation-lab/msk_access/cluster_access.mk)
#==================================================
# FASTQ / BAM file aligners
#==================================================
TARGETS += bwa_mem
bwa_mem :
$(call RUN_MAKE,innovation-lab/fastq_aligners/bwa_mem.mk)
TARGETS += bwa_par
bwa_par :
$(call RUN_MAKE,innovation-lab/fastq_aligners/bwa_parallel.mk)
TARGETS += bismark_bt2
bismark_bt2 :
$(call RUN_MAKE,innovation-lab/fastq_aligners/bismark_bt2.mk)
TARGETS += star_align
star_align :
$(call RUN_MAKE,innovation-lab/fastq_aligners/star_align.mk)
#==================================================
# BAM file utilities
#==================================================
TARGETS += merge_alignments
merge_alignments :
$(call RUN_MAKE,innovation-lab/bam_tools/merge_alignments.mk)
TARGETS += unmap_fasta
unmap_fasta :
$(call RUN_MAKE,innovation-lab/bam_tools/unmap_fasta.mk)
TARGETS += unmap_bam
unmap_bam :
$(call RUN_MAKE,innovation-lab/bam_tools/unmap_bam.mk)
TARGETS += merge_bam
merge_bam :
$(call RUN_MAKE,innovation-lab/bam_tools/merge_bam.mk)
#==================================================
# FASTQ file utilities
#==================================================
TARGETS += extract_fastq
extract_fastq :
$(call RUN_MAKE,innovation-lab/fastq_tools/extract_fastq.mk)
TARGETS += merge_fastq
merge_fastq :
$(call RUN_MAKE,innovation-lab/fastq_tools/merge_fastq.mk)
TARGETS += subsample_fastq
subsample_fastq :
$(call RUN_MAKE,innovation-lab/fastq_tools/subsample_fastq.mk)
#==================================================
# VCF file utilities
#==================================================
TARGETS += annotate_vcf_context
annotate_vcf_context :
$(call RUN_MAKE,innovation-lab/vcf_tools/annotate_vcf_context.mk)
TARGETS += annotate_vcf_maf
annotate_vcf_maf :
$(call RUN_MAKE,innovation-lab/vcf_tools/annotate_vcf_maf.mk)
TARGETS += annotate_maf_vcf
annotate_maf_vcf :
$(call RUN_MAKE,innovation-lab/vcf_tools/annotate_maf_vcf.mk)
#==================================================
# Copy number aberration callers
#==================================================
TARGETS += facets
facets :
$(call RUN_MAKE,innovation-lab/copy_number/facets.mk)
TARGETS += ascat
ascat :
$(call RUN_MAKE,innovation-lab/copy_number/ascat.mk)
TARGETS += cnvkit
cnvkit :
$(call RUN_MAKE,innovation-lab/copy_number/cnvkit.mk)
#==================================================
# RNA structural variant/fusion callers
#==================================================
TARGETS += arriba
arriba :
$(call RUN_MAKE,innovation-lab/structural_variants/arriba.mk)
TARGETS += defuse
defuse :
$(call RUN_MAKE,innovation-lab/structural_variants/defuse.mk)
TARGETS += fusion_catcher
fusion_catcher :
$(call RUN_MAKE,innovation-lab/structural_variants/fusioncatcher.mk)
TARGETS += star_fusion
star_fusion :
$(call RUN_MAKE,innovation-lab/structural_variants/starfusion.mk)
TARGETS += onco_fuse
onco_fuse :
$(call RUN_MAKE,innovation-lab/structural_variants/oncofuse.mk)
#==================================================
# Quality control
#==================================================
TARGETS += rnaseq_metrics
rnaseq_metrics :
$(call RUN_MAKE,innovation-lab/qc/rnaseq_metrics.mk)
TARGETS += bam_metrics
bam_metrics :
$(call RUN_MAKE,innovation-lab/qc/bam_metrics.mk)
TARGETS += fast_qc
fast_qc :
$(call RUN_MAKE,innovation-lab/qc/fast_qc.mk)
TARGETS += cluster_samples
cluster_samples :
$(call RUN_MAKE,innovation-lab/qc/cluster_samples.mk)
#==================================================
# RNA sequencing
#==================================================
TARGETS += umi_tools
umi_tools :
$(call RUN_MAKE,innovation-lab/rna_seq/umi_tools.mk)
TARGETS += kallisto
kallisto :
$(call RUN_MAKE,innovation-lab/rna_seq/kallisto.mk)
TARGETS += sum_reads
sum_reads :
$(call RUN_MAKE,innovation-lab/rna_seq/sum_reads.mk)
#==================================================
# BETA testing
#==================================================
TARGETS += pileup_metrics
pileup_metrics :
$(call RUN_MAKE,innovation-lab/beta_test/pileup_metrics.mk)
TARGETS += get_basecount
get_basecount :
$(call RUN_MAKE,innovation-lab/beta_test/get_basecount.mk)
TARGETS += msi_sensor
msi_sensor :
$(call RUN_MAKE,innovation-lab/beta_test/msi_sensor.mk)
TARGETS += sufam_genotype
sufam_genotype :
$(call RUN_MAKE,innovation-lab/beta_test/sufam_genotype.mk)
.PHONY : $(TARGETS)