Loading test/run_tests_icell8.sh +68 −1 Original line number Original line Diff line number Diff line Loading @@ -6,7 +6,7 @@ cd $(dirname ${BASH_SOURCE[0]})/.. cd $(dirname ${BASH_SOURCE[0]})/.. # used to export to PATH for testing on SGE server # used to export to PATH for testing on SGE server #export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` cellrangerpath=`which cellranger` Loading Loading @@ -37,3 +37,70 @@ bash launch_universc.sh --id "test-icell8-custom" --technology "iCell8" \ if [[ -f test/shared/icell8-test/*fastq ]]; then if [[ -f test/shared/icell8-test/*fastq ]]; then gzip -f test/shared/icell8-test/*fastq gzip -f test/shared/icell8-test/*fastq fi fi # call on icell8 files with custom whitelist and non-standard file names bash launch_universc.sh --setup -t "icell8" --barcodefile "test/shared/icell8-test/BarcodeList.txt" bash launch_universc.sh --id "test-icell8-72618_A375-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" "test/shared/icell8-test/72618_A375_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" "test/shared/icell8-test/72618_A375_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_A375-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_HCT116-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_HCT116-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-test-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/test_L001_R1_001.fastq" "test/shared/icell8-test/test_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/test_L001_R2_001.fastq" "test/shared/icell8-test/test_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-test-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/test_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/test_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" Loading
test/run_tests_icell8.sh +68 −1 Original line number Original line Diff line number Diff line Loading @@ -6,7 +6,7 @@ cd $(dirname ${BASH_SOURCE[0]})/.. cd $(dirname ${BASH_SOURCE[0]})/.. # used to export to PATH for testing on SGE server # used to export to PATH for testing on SGE server #export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` cellrangerpath=`which cellranger` Loading Loading @@ -37,3 +37,70 @@ bash launch_universc.sh --id "test-icell8-custom" --technology "iCell8" \ if [[ -f test/shared/icell8-test/*fastq ]]; then if [[ -f test/shared/icell8-test/*fastq ]]; then gzip -f test/shared/icell8-test/*fastq gzip -f test/shared/icell8-test/*fastq fi fi # call on icell8 files with custom whitelist and non-standard file names bash launch_universc.sh --setup -t "icell8" --barcodefile "test/shared/icell8-test/BarcodeList.txt" bash launch_universc.sh --id "test-icell8-72618_A375-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" "test/shared/icell8-test/72618_A375_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" "test/shared/icell8-test/72618_A375_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_A375-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_A375_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_A375_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_HCT116-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" "test/shared/icell8-test/72618_HCT116_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_HCT116-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_HCT116_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_HCT116_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" "test/shared/icell8-test/72618_NCI-H2452_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-72618_NCI-H2452-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/72618_NCI-H2452_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/72618_NCI-H2452_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-test-2-lanes" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/test_L001_R1_001.fastq" "test/shared/icell8-test/test_L002_R1_001.fastq" \ --read2 "test/shared/icell8-test/test_L001_R2_001.fastq" "test/shared/icell8-test/test_L002_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge" bash launch_universc.sh --id "test-icell8-test-1-lane" --technology "iCell8" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/icell8-test/test_L001_R1_001.fastq" \ --read2 "test/shared/icell8-test/test_L001_R2_001.fastq" \ --barcodefile "test/shared/icell8-test/WellList.txt" \ --jobmode "sge"
