correct inputs for crconveter (d75ef5ed) · Commits · github_fork / Universc

Dockerfile

+0 −1

Original line number	Diff line number	Diff line
		@@ -20,7 +20,6 @@ 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 ..

crconverter_open.sh

+46 −27

Original line number	Diff line number	Diff line
		@@ -72,6 +72,7 @@ output=""
		pipestance=""
		metrics=""
		analysis=""
		matrix=""
		aggregation=""
		gemgroups=""
		contiginfo=""
		@@ -84,16 +85,16 @@ description=""
		next=false
		end=false

		# crconverter tiny SC_RNA_COUNTER_CS --matrix /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u00fa679091/files/filtered_matrices_h5.h5 \
		# --analysis /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u00fa67911f/files/analysis/analysis.h5 \
		# --output /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/output_for_cloupe.cloupe \
		# --description CellRangerTest \
		# --metrics /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/join-u00fa679151/files/metrics_summary_json.json \
		# --gemgroups /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/gem_group_index_json.json



		if [[ $1 == "-h" ]] \|\| [[ $2 == "-h" ]] \|\| [[ $1 == "--help" ]] \|\| [[ $2 == "--help" ]]; then
		end=true
		usage=true
		help=true
		fi

		if [[ $1 == "-v" ]] \|\| [[ $2 == "-v" ]] \|\| [[ $1 == "--version" ]] \|\| [[ $2 == "--version" ]]; then
		end=true
		version=true
		fi
		for op in "${@:3}"; do
		if $next; then
		next=false;
		@@ -150,6 +151,16 @@ for op in "${@:3}"; do
		analysis=""
		fi
		;;
		--matrix)
		shift
		if [[ "$1" != "" ]]; then
		matrix="${1/%\//}"
		next=true
		shift
		else
		matrix=""
		fi
		;;
		--aggregation)
		shift
		if [[ "$1" != "" ]]; then
		@@ -252,7 +263,7 @@ for op in "${@:3}"; do
		shift
		;;
		-*)
		echo "$statement"
		echo "Error: Invalid option: $op"
		exit 1
		;;
		esac
		@@ -264,29 +275,37 @@ if [[ -z $1 ]]; then
		exit 1
		fi

		if [[ -z $help ]]; then
		if [[ $end ]]; then
		if [[ ! -z $help ]]; then
		echo "$statement"
		echo "$options"
		exit 0
		fi
		fi

		if [[ -z $version ]]; then
		if [[ $end ]]; then
		if [[ ! -z $version ]]; then
		echo "$crconverterversion"
		exit 0
		fi
		fi

		##########

		echo "Cloupe File not generated"
		exit 0

		#Wrote .cloupe file to /home/tom/datasets/20190717_Plant_Protoplast_fiveprime_HiSeq/test_AtRTD2_P09_PE/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u4b566787c3/files/output_for_cloupe.cloupe
		if [[ -z $output ]]; then
		echo "An output file must be specified"
		exit 1
		fi

		# crconverter tiny SC_RNA_COUNTER_CS --matrix /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/join-u00fa679091/files/filtered_matrices_h5.h5 \
		# --analysis /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SC_RNA_ANALYZER/SUMMARIZE_ANALYSIS/fork0/join-u00fa67911f/files/analysis/analysis.h5 \
		# --output /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/output_for_cloupe.cloupe \
		# --description CellRangerTest \
		# --metrics /root/tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/SUMMARIZE_REPORTS/fork0/join-u00fa679151/files/metrics_summary_json.json \
		# --gemgroups /root/tiny/SC_RNA_COUNTER_CS/CLOUPE_PREPROCESS/fork0/chnk0-u3dd5684351/files/gem_group_index_json.json
		if [[ ! -f $output ]]; then
		echo "#!/bin/bash" > $output
		echo "echo \"Please use the supported release of cellranger if you wish to use .cloupe files\"" >> $output
		chmod 755 $output
		else
		echo ".cloupe file already exists in $output"
		fi

		echo "Wrote .cloupe file to $output"
		echo "Warning .cloupe file may be dysfunctional"
		exit 0

Admin message