correct test scripts to run automatically (221b86a2) · Commits · github_fork / Universc

test/run_tests_10x.sh

+16 −2

Original line number	Diff line number	Diff line
		@@ -42,6 +42,9 @@ if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barco
		gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
		fi
		rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
		if [[ -d tiny-test ]]; then
		rm -rf tiny-test
		fi
		# test cellranger call
		cellranger testrun --id="tiny-test"
		# unzip input data
		@@ -58,7 +61,9 @@ fi
		if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then
		gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
		fi
		if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then
		rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
		fi
		cellranger count --id="tiny-count-v3" \
		--fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0"
		@@ -68,7 +73,9 @@ fi
		if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then
		gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
		fi
		if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then
		rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
		fi
		cellranger count --id="tiny-count-v2" \
		--fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0"
		@@ -80,6 +87,13 @@ fi
		if [[ -d input4cellranger_test-10x-v3 ]]; then
		rm -rf input4cellranger_test-10x-v3
		fi
		# unzip input data
		if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz ]]; then
		unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001/*fastq.gz
		fi
		if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz ]]; then
		unpigz -f test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002/*fastq.gz
		fi
		bash launch_universc.sh --id "test-10x-v3" --technology "10x" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--file "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \

test/run_tests_dropseq.sh

+10 −9

Original line number	Diff line number	Diff line
		@@ -18,12 +18,10 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[
		rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
		fi

		unpigz -k test/shared/dropseq-test/SRR1873277*fastq.gz

		## test drop-seq data
		# unzip input data
		if [[ -f test/shared/dropseq-test/*fastq.gz ]]; then
		gunzip -f test/shared/dropseq-test/*fastq.gz
		unpigz -f test/shared/dropseq-test/*fastq.gz
		fi
		# test manual setup
		bash launch_universc.sh -t "nadia" --setup
		@@ -35,12 +33,15 @@ fi
		if [[ -d input4cellranger_test-dropseq ]]; then
		rm -rf input4cellranger_test-dropseq
		fi
		if [[ -d test-dropseq ]]; then
		rm -rf test-dropseq
		fi

		# call on dropseq with files
		bash launch_universc.sh --id "test-dropseq" --technology "nadia" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--read1 "test/shared/dropseq-test/SRR1873277_Sample1_R1" \
		--read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2" \
		--verbose
		--read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2"

		# reset test data (compress)
		if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq ]]; then

test/run_tests_icell8.sh

+3 −3

Original line number	Diff line number	Diff line
		@@ -33,7 +33,7 @@ if [ -f test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq ]; then
		rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq
		fi
		if [ -d test-icell8-72618-KU812-2-lanes ];then
		rm -rf test-icell8-72618-KU812-2-lanes
		rm -rf test-icell8-72618_KU812-2-lanes
		fi
		bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCell8" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		@@ -47,8 +47,8 @@ fi
		if [ -f test/shared/icell8-test/KU812_S1_L001_R2_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq
		fi
		if [ -d test-icell8-KU812-1-lane ];then
		rm -rf test-icell8-KU812-1-lane
		if [ -d test-icell8-72618_KU812-1-lane ]; then
		rm -rf test-icell8-72618_KU812-1-lane
		fi
		bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCell8" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

launch_universc.sh

+1 −1

File changed.

Contains only whitespace changes.

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