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Copy pathgen.go
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176 lines (144 loc) · 6.02 KB
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package main
import (
"fmt"
"os"
"text/template"
"log"
)
/*
tt_EXTRA := -C tt -e BASE_URL="" -e REF_URL=""
r9.4-ecoli-loman_EXTRA := -C r9.4-ecoli-loman -e BASE_URL="http://s3.climb.ac.uk/nanopore" -e REF_URL="https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on"
r9.4-ecoli-simpson_EXTRA := -C r9.4-ecoli-simpson -e BASE_URL="INVALID!!!" -e REF_URL="https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=1356591284&extrafeat=976&conwithfeat=on&hide-sequence=on"
r9.4-human-chr21_EXTRA:= -C r9.4-human-chr21 -e BASE_URL="http://s3.amazonaws.com/nanopore-human-wgs" -e REF_URL="https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=fasta&id=568815577&extrafeat=976&conwithfeat=on&hide-sequence=on"
r9.4-leggett_EXTRA:= -C "r9.4-arabidopsis_thaliana-leggett" -e BASE_URL="" -e REF_URL=""
r9.4-sample_EXTRA := -C r9.4-sample -e BASE_URL="" -e 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'
.PHONY: sample-tt clean-tt
sample-%:
@$(MAKE) --no-print-directory $($*_EXTRA) -L sample -f ../single.Makefile
# @$(MAKE) --no-print-directory $($*_EXTRA) -L ref.fasta -f ../single.Makefile
clean-%:
@$(MAKE) --no-print-directory $($*_EXTRA) clean -f ../single.Makefile
check-%:
@$(MAKE) --no-print-directory $($*_EXTRA) check-raw -f ../single.Makefile
# @$(MAKE) --no-print-directory $($*_EXTRA) check-extracted -f ../single.Makefile
create-check-%:
@$(MAKE) --no-print-directory $($*_EXTRA) --always-make checksum.raw.sha512 -f ../single.Makefile
# @$(MAKE) --no-print-directory $($*_EXTRA) --always-make checksum.extracted.sha512 -f ../single.Makefile
*/
const tmpl = `
{{- $extra := printf "-C %s -e BASE_URL='%s' REF_URL='%s'" .Folder .BaseURL .RefURL -}}
{{ .Name }}-make-sample:
{{ print "\t" -}} @$(MAKE) --no-print-directory {{ $extra }} -L sample -f ../single.Makefile
.PHONY: {{ .Name }}-make-sample
{{ .Name }}-download_ref:
{{ print "\t" -}} @$(MAKE) --no-print-directory {{ $extra }} -L sample -f ../single.Makefile
.PHONY: {{ .Name }}-download_ref
{{ .Name }}-clean:
{{ print "\t" -}}@$(MAKE) --no-print-directory {{ $extra }} clean -f ../single.Makefile
.PHONY: {{ .Name }}-clean
{{ .Name }}-check:
{{ print "\t" -}}@$(MAKE) --no-print-directory {{ $extra }} check-raw -f ../single.Makefile
.PHONY: {{ .Name }}-check
{{ .Name }}-create-check:
{{ print "\t" -}}@$(MAKE) --no-print-directory {{ $extra }} --always-make checksum.raw.sha512 -f ../single.Makefile
.PHONY: {{ .Name }}-create-check
{{ .Name }}-chiron_basecall:
{{ print "\t" -}} @$(MAKE) --no-print-directory {{ $extra }} -L chiron_basecall -f ../single.Makefile
.PHONY: {{ .Name }}-chiron_basecall
{{ .Name }}-align:
{{ print "\t" -}} @$(MAKE) --no-print-directory {{ $extra }} -L alignment.sam -f ../single.Makefile
.PHONY: {{ .Name }}-align
{{ .Name }}-prepare_dataset:
{{ print "\t" -}} @$(MAKE) --no-print-directory {{ $extra }} -L prepare_dataset -f ../single.Makefile
.PHONY: {{ .Name }}-prepare_dataset
`
type Item struct {
Name string // Alias for running
BaseURL string // BaseURL for downloading raw files
RefURL string // URL for downloading ref.fasta, that is reference genome
Folder string // Folder where all data should be saved/processed
}
const EColiRef = "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"
func main() {
fmt.Println(`
.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
`)
t := template.Must(template.New("x").Parse(tmpl))
for _, f := range []Item{
{
Name: "sample",
Folder: "r9.4-sample",
RefURL: EColiRef,
BaseURL: "MISSING!",
},
{
Name: "ecoli-loman",
Folder: "r9.4-ecoli-loman",
RefURL: EColiRef,
BaseURL: "http://s3.climb.ac.uk/nanopore",
},
{
Name: "ecoli-simpson",
Folder: "r9.4-ecoli-simpson",
RefURL: EColiRef,
BaseURL: "MISSING",
},
{
Name: "arabidopsis_thaliana-leggett",
Folder: "r9.4-arabidopsis_thaliana-leggett",
RefURL: "Unknown",
BaseURL: "MISSING",
},
} {
if f.Name != "" {
if err := t.Execute(os.Stdout, f); err != nil {
log.Fatal(err)
}
}
// for aliased datasets
if f.Name != f.Folder {
f.Name = f.Folder
if err := t.Execute(os.Stdout, f); err != nil {
log.Fatal(err)
}
}
}
}