remove STAR reference and generate with GNU Make

SHELL := /bin/bash -O extglob

VERSION=$(shell git describe --tags --always --dirty)

export ROOT_DIR=$(shell pwd)

# Targets for development builds.

#

all: reference

clean: reference-clean

# Targets for python builds

# Find python libs, includes, and default flags.

PYTHON_ROOT:=$(shell python-config --exec-prefix)

PYTHON_LIB_DIR:=$(dir $(lastword $(wildcard $(PYTHON_ROOT)/lib*/libpython*.so*)))

PYTHON_SITE_PKG:=$(lastword $(wildcard $(PYTHON_LIB_DIR)/python*/site-packages))

PYTHON_CFLAGS:=$(shell python-config --cflags)

PYTHON_LDFLAGS:=$(shell python-config --ldflags)

reference:

	make -C  test/cellranger_reference/cellranger-tiny-ref

reference-clean:

	make -C  test/cellranger_reference/cellranger-tiny-ref clean

        echo "removing pre-generated cellranger reference files"

        rm -Rf  test/cellranger_reference/cellranger-tiny-ref/3.0.0

        rm -Rf  test/cellranger_reference/cellranger-tiny-ref/1.2.0

#!/bin/bash

PWD=$(shell pwd)

all: $(EXEC)

louvain:

	echo "generating cellranger references"

	cellranger mkref --genome=1.2.0 --fasta=genome-1.2.0.fa --genes=genes-1.2.0.gtf

	rm -rf genome-1.2.0.fa genes-1.2.0.gtf

	cellranger mkref --genome=3.0.0 --fasta=genome-3.0.0.fa --genes=genes-3.0.0.gtf

	rm -rf genome-3.0.0.fa genes-3.0.0.gtf

##########################################

# Generic rules

##########################################

%.o: %.cpp %.h

	$(CXX) -o  $@ -c $< $(CXXFLAGS)

%.o: %.cpp

	$(CXX) -o $@ -c $< $(CXXFLAGS)

clean:

	echo "moving fasta and gtf from cellranger reference"

	mv 1.2.0/fasta/genome.fa genome-1.2.0.fa

	mv 1.2.0/genes/genes.gtf genes-1.2.0.gtf

	mv 3.0.0/fasta/genome.fa genome-3.0.0.fa

	mv 3.0.0/genes/genes.gtf genes-3.0.0.gtf

mrproper: clean

        rm -f *~ $(EXEC)