diff --git a/generated/bioc2024bamSliceR.Dockerfile b/generated/bioc2024bamSliceR.Dockerfile new file mode 100644 index 0000000..a95ce20 --- /dev/null +++ b/generated/bioc2024bamSliceR.Dockerfile @@ -0,0 +1,2 @@ +FROM ghcr.io/bioconductor/bioconductor:devel +RUN sudo apt-get update && sudo apt-get -y install apt-file && echo trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr | 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)" diff --git a/generated/bioc2024bamSliceR.container b/generated/bioc2024bamSliceR.container new file mode 100644 index 0000000..eac5510 --- /dev/null +++ b/generated/bioc2024bamSliceR.container @@ -0,0 +1 @@ +ghcr.io/bioconductor/workshop-contributions:devel-dabb9c4e diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml index ee03988..2e4d564 100644 --- a/generated/workshop-values.yaml +++ b/generated/workshop-values.yaml @@ -1,5 +1,5 @@ extraFileMappings: - /galaxy/server/tools/interactive/biocworkshop_vjcontobioc2024.xml: + /galaxy/server/tools/interactive/biocworkshop_eurobioc2024isee.xml: useSecret: false applyToJob: true applyToSetupJob: true @@ -8,13 +8,13 @@ extraFileMappings: applyToNginx: true tpl: false content: | - - Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN + + Interactive SummarizedExperiment Explorer - ghcr.io/vjcitn/ontoprocws:latest + ghcr.io/isee/iseedemoeurobioc2024:latest - + 8787 @@ -25,12 +25,12 @@ extraFileMappings: $__galaxy_url__ - export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/ontoProcWS/vignettes/owlents.Rmd' ]; then echo '/home/rstudio/ontoProcWS/vignettes/owlents.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/owlents.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; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init + export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/iSEEDemoEuroBioC2024/vignettes/workshop_isee_extension.Rmd' ]; then echo '/home/rstudio/iSEEDemoEuroBioC2024/vignettes/workshop_isee_extension.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/workshop_isee_extension.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; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; 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/vjcitn/ontoProcWS. + This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/iSEE/iSEEDemoEuroBioC2024.