From 542ec664aad1225ddaf79b108cffc386d0d59bcd Mon Sep 17 00:00:00 2001 From: github-actions Date: Wed, 19 Jul 2023 00:52:55 +0000 Subject: [PATCH] Push generated bioc2023cytoverse --- generated/bioc2023cytoverse.Dockerfile | 3 --- generated/bioc2023cytoverse.container | 2 +- generated/workshop-values-bioc2023cytoverse.yaml | 10 +++++----- generated/workshop-values.yaml | 10 +++++----- 4 files changed, 11 insertions(+), 14 deletions(-) delete mode 100644 generated/bioc2023cytoverse.Dockerfile diff --git a/generated/bioc2023cytoverse.Dockerfile b/generated/bioc2023cytoverse.Dockerfile deleted file mode 100644 index a6b3a2f..0000000 --- a/generated/bioc2023cytoverse.Dockerfile +++ /dev/null @@ -1,3 +0,0 @@ -FROM ghcr.io/bioconductor/bioconductor:3.17 -RUN sudo apt-get update && sudo apt-get -y install apt-file && echo LieberInstitute/SPEAQeasyWorkshop2023 | tr ',' '\n' > /tmp/pkglist && cat /tmp/pkglist | xargs -i Rscript -e "if (!require('rspm')) { install.packages('rspm'); rspm::enable(); }; p = BiocManager::install(c('{}'), dependencies = c('Depends', 'Imports', 'LinkingTo', 'Suggests')); if(p %in% rownames(installed.packages())) q(status = 0) else if(strsplit(p, '/')[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)" -RUN sudo apt-get update && sudo apt-get -y install apt-file && cd /home/rstudio && echo "vignettes/*" | tr ',' '\n' > vignlist && git clone https://github.com/LieberInstitute/SPEAQeasyWorkshop2023 && cp -r SPEAQeasyWorkshop2023 tmpsource && cd tmpsource && curl -o install.sh https://raw.githubusercontent.com/Bioconductor/workshop-contributions/main/.github/scripts/install_missing.sh && cat ../vignlist | xargs -i bash install.sh {} && cd .. && rm -rf vignlist tmpsource/ diff --git a/generated/bioc2023cytoverse.container b/generated/bioc2023cytoverse.container index 09790ab..7b7aeec 100644 --- a/generated/bioc2023cytoverse.container +++ b/generated/bioc2023cytoverse.container @@ -1 +1 @@ -ghcr.io/bioconductor/workshop-contributions:3.17-5cb5eb3a +ghcr.io/ozettetech/cytoverse-bioc-2023:latest diff --git a/generated/workshop-values-bioc2023cytoverse.yaml b/generated/workshop-values-bioc2023cytoverse.yaml index 053b38d..f7774bd 100644 --- a/generated/workshop-values-bioc2023cytoverse.yaml +++ b/generated/workshop-values-bioc2023cytoverse.yaml @@ -7,10 +7,10 @@ applyToNginx: true tpl: false content: | - - a Scalable Pipeline for Expression Analysis and Quantification + + with the cytoverse - ghcr.io/bioconductor/workshop-contributions:3.17-feab579d + ghcr.io/ozettetech/cytoverse-bioc-2023:latest @@ -24,12 +24,12 @@ $__galaxy_url__ - if [ -f '/home/rstudio/SPEAQeasyWorkshop2023/vignettes/SPEAQeasyWorkshop2023.Rmd' ]; then echo '/home/rstudio/SPEAQeasyWorkshop2023/vignettes/SPEAQeasyWorkshop2023.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/SPEAQeasyWorkshop2023.Rmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init + if [ -f '/home/rstudio/cytoverse-bioc-2023/vignettes/Import_fcs.Rmd' ]; then echo '/home/rstudio/cytoverse-bioc-2023/vignettes/Import_fcs.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/Import_fcs.Rmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init - This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/LieberInstitute/SPEAQeasyWorkshop2023. + This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/OzetteTech/cytoverse-bioc-2023. diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml index 11ff65b..9a70817 100644 --- a/generated/workshop-values.yaml +++ b/generated/workshop-values.yaml @@ -8,10 +8,10 @@ extraFileMappings: applyToNginx: true tpl: false content: | - - a Scalable Pipeline for Expression Analysis and Quantification + + with the cytoverse - ghcr.io/bioconductor/workshop-contributions:3.17-feab579d + ghcr.io/ozettetech/cytoverse-bioc-2023:latest @@ -25,12 +25,12 @@ extraFileMappings: $__galaxy_url__ - if [ -f '/home/rstudio/SPEAQeasyWorkshop2023/vignettes/SPEAQeasyWorkshop2023.Rmd' ]; then echo '/home/rstudio/SPEAQeasyWorkshop2023/vignettes/SPEAQeasyWorkshop2023.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/SPEAQeasyWorkshop2023.Rmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init + if [ -f '/home/rstudio/cytoverse-bioc-2023/vignettes/Import_fcs.Rmd' ]; then echo '/home/rstudio/cytoverse-bioc-2023/vignettes/Import_fcs.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/Import_fcs.Rmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init - This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/LieberInstitute/SPEAQeasyWorkshop2023. + This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/OzetteTech/cytoverse-bioc-2023.