## ----install, eval = FALSE---------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("BiocDockerManager") ## ----load, echo = TRUE, message=FALSE----------------------------------------- library(BiocDockerManager) library(dplyr) ## ----do_it-------------------------------------------------------------------- .is_docker_installed <- function() { code <- suppressWarnings( system("docker --version", ignore.stderr = TRUE, ignore.stdout = TRUE) ) code == 0 } ## execute code if the date is later than a specified day do_it = BiocDockerManager:::.is_docker_installed() ## ----available1, eval=TRUE---------------------------------------------------- BiocDockerManager::available() ## ----------------------------------------------------------------------------- res <- BiocDockerManager::available() res %>% select(IMAGE, DESCRIPTION, TAGS) %>% filter(IMAGE == "bioconductor_docker") ## ----available2--------------------------------------------------------------- res2 <- BiocDockerManager::available(pattern = "bioconductor_docker") res2 %>% select(IMAGE, DESCRIPTION, TAGS) ## ----deprecated, eval = TRUE-------------------------------------------------- BiocDockerManager::available(deprecated=TRUE) %>% select(IMAGE, DESCRIPTION) ## ----help, eval = TRUE-------------------------------------------------------- if(do_it) { BiocDockerManager::help() } ## ----pull, eval = TRUE-------------------------------------------------------- if (do_it) { BiocDockerManager::install( repository = "bioconductor/bioconductor_docker", tag = "latest" ) } ## ----installed, eval = TRUE--------------------------------------------------- if (do_it) BiocDockerManager::installed() ## ----filter-installed, eval = TRUE-------------------------------------------- if (do_it) BiocDockerManager::installed( repository = "bioconductor/bioconductor_docker" ) ## ----label-maintainer, eval = TRUE-------------------------------------------- if (do_it) { ## Get version for the "latest" tag bioconductor image BiocDockerManager::maintainer( repository = "bioconductor/bioconductor_docker", tag = "latest" ) ## The above functions works the same as BiocDockerManager::maintainer(tag = "latest") } ## ----label-version, eval = TRUE----------------------------------------------- if(do_it) { BiocDockerManager::version( repository = "bioconductor/bioconductor_docker", tag = "latest" ) ## Get image version BiocDockerManager::version(tag = "latest") BiocDockerManager::version(tag = "devel") BiocDockerManager::version(tag = "RELEASE_3_10") } ## ----valid, eval = TRUE------------------------------------------------------- if(do_it) { BiocDockerManager::valid( repository = "bioconductor/bioconductor_docker", tag = "latest" ) } ## ----template, eval = FALSE--------------------------------------------------- # BiocDockerManager::use_dockerfile() ## ----workflow-1, eval = TRUE-------------------------------------------------- if (do_it) { ## 1. Check available images BiocDockerManager::available() ## 2. Install a new image BiocDockerManager::install( repository = "bioconductor/bioconductor_docker", tag = "devel" ) } ## ----workflow-2, eval = TRUE-------------------------------------------------- if (do_it) { ## 3. Check if image is valid BiocDockerManager::valid( "bioconductor/bioconductor_docker", tag = "devel" ) ## 4. Download update to image BiocDockerManager::install( "bioconductor/bioconductor_docker", tag = "devel" ) ## 5. Check version BiocDockerManager::version( "bioconductor/bioconductor_docker", tag = "devel" ) } ## ----sessionInfo-------------------------------------------------------------- sessionInfo()