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301 lines (231 loc) · 21.9 KB
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.FORCE:
proto: .FORCE
python -m grpc_tools.protoc -I $$(pwd)/protos --mypy_out=./minion_data --python_out=./minion_data $$(pwd)/protos/*
USERNAME=""
TAG="latest"
ifeq ($(strip $(USERNAME)), "")
BASE_TAG=""
else
BASE_TAG=$(USERNAME)/
endif
docker-build:
docker build -t $(BASE_TAG)minion_data:$(TAG) .
.PHONY: docker-build
docker-push: docker-build
docker push $(BASE_TAG)minion_data:$(TAG)
.PHONY: docker-push
pypi-publish:
python setup.py bdist_wheel && twine upload dist/*
.PHONY: pypi-publish
# Reference hybrid assembly
rwick_basecaller/01_raw_fast5/barcode01.fasta.gz:
@mkdir -p rwick_basecaller/01_raw_fast5
wget https://ndownloader.figshare.com/files/8810704 -O $@
# Illumina reads
rwick_basecaller/01_raw_fast5/barcode01_1.fastq.gz:
@mkdir -p rwick_basecaller/01_raw_fast5
wget https://ndownloader.figshare.com/files/8811145 -O $@
rwick_basecaller/01_raw_fast5/barcode01_2.fastq.gz:
@mkdir -p rwick_basecaller/01_raw_fast5
wget https://ndownloader.figshare.com/files/8811148 -O $@
# Raw fast5 files
rwick_basecaller/01_raw_fast5/INF042_raw_fast5.tar:
@mkdir -p rwick_basecaller/01_raw_fast5
wget https://ndownloader.figshare.com/files/9199063 -O $@
rwick_basecaller/.done: rwick_basecaller/01_raw_fast5/barcode01_2.fastq.gz rwick_basecaller/01_raw_fast5/barcode01_1.fastq.gz rwick_basecaller/01_raw_fast5/barcode01.fasta.gz rwick_basecaller/01_raw_fast5/INF042_raw_fast5.tar
@mkdir -p rwick_basecaller/02_basecalled_reads
tar -xf rwick_basecaller/01_raw_fast5/INF042_raw_fast5.tar --directory rwick_basecaller/01_raw_fast5
@touch $@
rwick: rwick_basecaller/.done
sample-make-sample:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: sample-make-sample
sample-download_ref:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: sample-download_ref
sample-clean:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' clean -f ../single.Makefile
.PHONY: sample-clean
sample-check:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' check-raw -f ../single.Makefile
.PHONY: sample-check
sample-create-check:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: sample-create-check
sample-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L chiron_basecall -f ../single.Makefile
.PHONY: sample-chiron_basecall
sample-align:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L alignment.sam -f ../single.Makefile
.PHONY: sample-align
sample-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L prepare_dataset -f ../single.Makefile
.PHONY: sample-prepare_dataset
r9.4-sample-make-sample:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: r9.4-sample-make-sample
r9.4-sample-download_ref:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: r9.4-sample-download_ref
r9.4-sample-clean:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' clean -f ../single.Makefile
.PHONY: r9.4-sample-clean
r9.4-sample-check:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' check-raw -f ../single.Makefile
.PHONY: r9.4-sample-check
r9.4-sample-create-check:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: r9.4-sample-create-check
r9.4-sample-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L chiron_basecall -f ../single.Makefile
.PHONY: r9.4-sample-chiron_basecall
r9.4-sample-align:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L alignment.sam -f ../single.Makefile
.PHONY: r9.4-sample-align
r9.4-sample-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-sample -e BASE_URL='MISSING!' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L prepare_dataset -f ../single.Makefile
.PHONY: r9.4-sample-prepare_dataset
ecoli-loman-make-sample:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: ecoli-loman-make-sample
ecoli-loman-download_ref:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: ecoli-loman-download_ref
ecoli-loman-clean:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' clean -f ../single.Makefile
.PHONY: ecoli-loman-clean
ecoli-loman-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' check-raw -f ../single.Makefile
.PHONY: ecoli-loman-check
ecoli-loman-create-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: ecoli-loman-create-check
ecoli-loman-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L chiron_basecall -f ../single.Makefile
.PHONY: ecoli-loman-chiron_basecall
ecoli-loman-align:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L alignment.sam -f ../single.Makefile
.PHONY: ecoli-loman-align
ecoli-loman-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L prepare_dataset -f ../single.Makefile
.PHONY: ecoli-loman-prepare_dataset
r9.4-ecoli-loman-make-sample:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-make-sample
r9.4-ecoli-loman-download_ref:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-download_ref
r9.4-ecoli-loman-clean:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' clean -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-clean
r9.4-ecoli-loman-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' check-raw -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-check
r9.4-ecoli-loman-create-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-create-check
r9.4-ecoli-loman-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L chiron_basecall -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-chiron_basecall
r9.4-ecoli-loman-align:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L alignment.sam -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-align
r9.4-ecoli-loman-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-ecoli-loman -e BASE_URL='http://s3.climb.ac.uk/nanopore' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L prepare_dataset -f ../single.Makefile
.PHONY: r9.4-ecoli-loman-prepare_dataset
ecoli-simpson-make-sample:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: ecoli-simpson-make-sample
ecoli-simpson-download_ref:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: ecoli-simpson-download_ref
ecoli-simpson-clean:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' clean -f ../single.Makefile
.PHONY: ecoli-simpson-clean
ecoli-simpson-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' check-raw -f ../single.Makefile
.PHONY: ecoli-simpson-check
ecoli-simpson-create-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: ecoli-simpson-create-check
ecoli-simpson-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L chiron_basecall -f ../single.Makefile
.PHONY: ecoli-simpson-chiron_basecall
ecoli-simpson-align:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L alignment.sam -f ../single.Makefile
.PHONY: ecoli-simpson-align
ecoli-simpson-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L prepare_dataset -f ../single.Makefile
.PHONY: ecoli-simpson-prepare_dataset
r9.4-ecoli-simpson-make-sample:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-make-sample
r9.4-ecoli-simpson-download_ref:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L sample -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-download_ref
r9.4-ecoli-simpson-clean:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' clean -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-clean
r9.4-ecoli-simpson-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' check-raw -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-check
r9.4-ecoli-simpson-create-check:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-create-check
r9.4-ecoli-simpson-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L chiron_basecall -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-chiron_basecall
r9.4-ecoli-simpson-align:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L alignment.sam -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-align
r9.4-ecoli-simpson-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-ecoli-simpson -e BASE_URL='MISSING' REF_URL='https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on' -L prepare_dataset -f ../single.Makefile
.PHONY: r9.4-ecoli-simpson-prepare_dataset
arabidopsis_thaliana-leggett-make-sample:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L sample -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-make-sample
arabidopsis_thaliana-leggett-download_ref:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L sample -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-download_ref
arabidopsis_thaliana-leggett-clean:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' clean -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-clean
arabidopsis_thaliana-leggett-check:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' check-raw -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-check
arabidopsis_thaliana-leggett-create-check:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-create-check
arabidopsis_thaliana-leggett-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L chiron_basecall -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-chiron_basecall
arabidopsis_thaliana-leggett-align:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L alignment.sam -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-align
arabidopsis_thaliana-leggett-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L prepare_dataset -f ../single.Makefile
.PHONY: arabidopsis_thaliana-leggett-prepare_dataset
r9.4-arabidopsis_thaliana-leggett-make-sample:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L sample -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-make-sample
r9.4-arabidopsis_thaliana-leggett-download_ref:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L sample -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-download_ref
r9.4-arabidopsis_thaliana-leggett-clean:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' clean -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-clean
r9.4-arabidopsis_thaliana-leggett-check:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' check-raw -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-check
r9.4-arabidopsis_thaliana-leggett-create-check:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-create-check
r9.4-arabidopsis_thaliana-leggett-chiron_basecall:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L chiron_basecall -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-chiron_basecall
r9.4-arabidopsis_thaliana-leggett-align:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L alignment.sam -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-align
r9.4-arabidopsis_thaliana-leggett-prepare_dataset:
@$(MAKE) --no-print-directory -C r9.4-arabidopsis_thaliana-leggett -e BASE_URL='MISSING' REF_URL='Unknown' -L prepare_dataset -f ../single.Makefile
.PHONY: r9.4-arabidopsis_thaliana-leggett-prepare_dataset