clean up makefiles

 && apt-get upgrade -y \

 && apt-get install -y \

 git \

 git-lfs \

 make \

 gzip

RUN git clone "https://github.com/TomKellyGenetics/cellranger_convert.git"

RUN cd cellranger_convert/test/cellranger_reference/cellranger-tiny-ref/ \

 && git lfs pull

RUN cd cellranger_convert \

 && make reference \

 && cd .. 

reference:

	echo "generating cellranger references"

	@if [ "test" = "test" ]; then\

		echo "Hello world";\

	fi

	@if [ ! -d 1.2.0 ]; then\

		echo 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;\