Loading .github/workflows/docker-ci.yml +1 −1 Original line number Diff line number Diff line Loading @@ -50,7 +50,7 @@ jobs: push: true dianostics: diagnostics: runs-on: ubuntu-20.04 steps: - uses: actions/checkout@v2 Loading test/run_tests_10x_gh_actions.sh +3 −4 Original line number Diff line number Diff line Loading @@ -7,9 +7,8 @@ pwd cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 make test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/shared/dropseq-test/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ Loading test/run_tests_10x_v2_gh_actions.sh +3 −4 Original line number Diff line number Diff line Loading @@ -7,9 +7,8 @@ pwd cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 make test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 rm -rf test/shared/dropseq-test/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ Loading test/run_tests_cellranger_gh_actions.sh +3 −4 Original line number Diff line number Diff line Loading @@ -7,9 +7,8 @@ pwd cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 make test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/shared/dropseq-test/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ Loading test/run_tests_dropseq_gh_actions.sh +3 −8 Original line number Diff line number Diff line Loading @@ -10,16 +10,11 @@ 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')'` cellrangerpath=`which cellranger` # set up cellranger reference if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then ln $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA fi if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then ln $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA fi rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 # test manual setup bash launch_universc.sh -t "nadia" --setup Loading Loading
.github/workflows/docker-ci.yml +1 −1 Original line number Diff line number Diff line Loading @@ -50,7 +50,7 @@ jobs: push: true dianostics: diagnostics: runs-on: ubuntu-20.04 steps: - uses: actions/checkout@v2 Loading
test/run_tests_10x_gh_actions.sh +3 −4 Original line number Diff line number Diff line Loading @@ -7,9 +7,8 @@ pwd cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 make test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/shared/dropseq-test/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ Loading
test/run_tests_10x_v2_gh_actions.sh +3 −4 Original line number Diff line number Diff line Loading @@ -7,9 +7,8 @@ pwd cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 make test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 rm -rf test/shared/dropseq-test/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ Loading
test/run_tests_cellranger_gh_actions.sh +3 −4 Original line number Diff line number Diff line Loading @@ -7,9 +7,8 @@ pwd cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'` cellrangerpath=`which cellranger` rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0 make test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/shared/dropseq-test/* test/shared/mappa-test/ test/shared/icell8-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ Loading
test/run_tests_dropseq_gh_actions.sh +3 −8 Original line number Diff line number Diff line Loading @@ -10,16 +10,11 @@ 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')'` cellrangerpath=`which cellranger` # set up cellranger reference if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then ln $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA fi if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then ln $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA fi rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0 make -C test/cellranger_reference/cellranger-tiny-ref reference rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 rm -rf test/shared/dropseq-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/ test/shared/smartseq3-test/ test/shared/indrop-v3-test/ rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 # test manual setup bash launch_universc.sh -t "nadia" --setup Loading
