## ---- include = FALSE---------------------------------------------------- knitr::opts_chunk$set( eval = AnVIL::gcloud_exists(), collapse = TRUE, cache = TRUE ) options(width=75) ## ---- eval = FALSE------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager", repos = "https://cran.r-project.org") # BiocManager::install("AnVIL") ## ---- message =FALSE, eval = TRUE, cache = FALSE------------------------- library(AnVIL) ## ---- eval = FALSE------------------------------------------------------- # dir(file.path(Sys.getenv("GCLOUD_SDK_PATH"), "bin"), "^(gcloud|gsutil)$") # ## [1] "gcloud" "gsutil" ## ---- eval = TRUE-------------------------------------------------------- ## the code chunks in this vignette are fully evaluated when ## gcloud_exists() returns TRUE gcloud_exists() ## ---- eval = FALSE------------------------------------------------------- # AnVIL::install("GenomicFeatures") ## ---- eval = FALSE------------------------------------------------------- # add_libpaths("~/my/project") ## ------------------------------------------------------------------------ # gcloud_account() # authentication account # gcloud_project() # billing project information ## ------------------------------------------------------------------------ # gcloud_cmd("projects", "list") %>% # readr::read_table() %>% # filter(startsWith(PROJECT_ID, "anvil")) ## ---- eval = FALSE------------------------------------------------------- # gcloud_help("projects") ## ------------------------------------------------------------------------ # src <- "gs://genomics-public-data/1000-genomes/" ## ------------------------------------------------------------------------ # gsutil_ls(src) # # other <- paste0(src, "other") # gsutil_ls(other, recursive = TRUE) # # sample_info <- paste0(src, "other/sample_info/sample_info.csv") # gsutil_stat(sample_info) ## ------------------------------------------------------------------------ # fl <- tempfile() # gsutil_cp(sample_info, fl) # # csv <- readr::read_csv(fl, guess_max = 5000L, col_types = readr::cols()) # csv ## ------------------------------------------------------------------------ # pipe <- gsutil_pipe(fl, "rb") # readr::read_csv(pipe, guess_max = 5000L, col_types = readr::cols()) %>% # dplyr::select("Sample", "Family_ID", "Population", "Gender") ## ------------------------------------------------------------------------ # destination <- tempfile() # stopifnot(dir.create(destination)) # source <- paste0(src, "other/sample_info") # # ## dry run # gsutil_rsync(source, destination) # # gsutil_rsync(source, destination, dry = FALSE) # dir(destination, recursive = TRUE) # # ## nothing to synchronize # gsutil_rsync(source, destination, dry = FALSE) # # ## one file requires synchronization # unlink(file.path(destination, "README")) # gsutil_rsync(source, destination, dry = FALSE) ## ---- echo = FALSE, cache = FALSE---------------------------------------- # knitr::include_graphics('images/AnVIL-Workspace-Data.png') ## ---- include = FALSE, cache = FALSE------------------------------------- # avworkspace_namespace("pathogen-genomic-surveillance") # avworkspace_name("COVID-19") ## ------------------------------------------------------------------------ # avworkspace_namespace() # avworkspace_name() ## ------------------------------------------------------------------------ # ## N.B.: IT MAY NOT BE NECESSARY TO SET THESE WHEN ON ANVIL # avworkspace_namespace("pathogen-genomic-surveillance") # avworkspace_name("COVID-19") ## ------------------------------------------------------------------------ # avtables() # sample <- avtable("sample") # sample ## ------------------------------------------------------------------------ # sample %>% # select("sample_id", contains("fasta")) %>% # filter(!is.na(final_assembly_fasta)) ## ---- eval = FALSE------------------------------------------------------- # mtcars %>% # mutate(cyl = factor(cyl)) %>% # avtable_import() ## ---- eval = FALSE------------------------------------------------------- # ## editable copy of '1000G-high-coverage-2019' workspace # avworkspace("bioconductor-rpci-anvil/1000G-high-coverage-2019") # sample <- # avtable("sample") %>% # existing table # mutate(set = sample(head(LETTERS), nrow(.), TRUE)) # arbitrary groups # sample %>% # new 'participant_set' table # avtable_import_set("participant", "set", "participant") # sample %>% # new 'sample_set' table # avtable_import_set("sample", "set", "name") ## ------------------------------------------------------------------------ # avdata() ## ------------------------------------------------------------------------ # bucket <- avbucket() # bucket ## ------------------------------------------------------------------------ # avfiles_ls() ## ---- eval = FALSE------------------------------------------------------- # ## requires workspace ownership # uri <- avbucket() # discover bucket # bucket <- file.path(uri, "mtcars.tab") # write.table(mtcars, gsutil_pipe(bucket, "w")) # write to bucket ## ---- eval = FALSE------------------------------------------------------- # ## backup all files and folders in the current working directory # avfiles_backup(getwd(), recursive = TRUE) # # ## backup all files in the current directory # avfiles_backup(dir()) # # ## backup all files to gs:///scratch/ # avfiles_backup(dir, paste0(avbucket(), "/scratch")) ## ------------------------------------------------------------------------ # uri <- c( # vcf = "drs://dg.ANV0/6f633518-f2de-4460-aaa4-a27ee6138ab5", # tbi = "drs://dg.ANV0/4fb9e77f-c92a-4deb-ac90-db007dc633aa" # ) ## ---- eval = FALSE------------------------------------------------------- # tbl <- drs_stat(uri) # ## # A tibble: 2 × 9 # ## drs fileName size gsUri accessUrl timeUpdated hashes bucket name # ## # ## 1 drs://d… NA21144… 7.06e9 gs:/… NA 2020-07-08… fc-56… CCDG… # ## 2 drs://d… NA21144… 4.08e6 gs:/… NA 2020-07-08… fc-56… CCDG… ## ---- eval = FALSE------------------------------------------------------- # drs_cp(uri, "/tmp") # local temporary directory # drs_cp(uri, avbucket()) # workspace bucket ## ---- eval = FALSE------------------------------------------------------- # suppressPackageStartupMessages({ # library(VariantAnnotation) # }) # https <- drs_access_url(uri) # vcffile <- VcfFile(https[["vcf"]], https[["tbi"]]) # scanVcfHeader(vcffile) # ## class: VCFHeader # ## samples(1): NA21144 # ## meta(3): fileformat reference contig # ## fixed(2): FILTER ALT # ## info(16): BaseQRankSum ClippingRankSum ... ReadPosRankSum VariantType # ## geno(11): GT AB ... PL SB # # variants <- readVcf(vcffile, param = GRanges("chr1:1-1000000")) # nrow(variants) # ## [1] 123077 ## ------------------------------------------------------------------------ # terra <- Terra() ## ------------------------------------------------------------------------ # terra ## ------------------------------------------------------------------------ # terra %>% tags("Status") ## ------------------------------------------------------------------------ # terra$status # terra$status() ## ------------------------------------------------------------------------ # args(terra$createBillingProjectFull) ## ------------------------------------------------------------------------ # args(terra$overwriteWorkspaceMethodConfig) ## ------------------------------------------------------------------------ # status <- terra$status() # class(status) ## ------------------------------------------------------------------------ # str(status) ## ------------------------------------------------------------------------ # lst <- status %>% as.list() # lengths(lst) # lengths(lst$systems) # str(lst$systems) ## ------------------------------------------------------------------------ # .MyService <- setClass("MyService", contains = "Service") # # MyService <- # function() # { # .MyService(Service( # "myservice", # host = "api.firecloud.org", # api_url = "https://api.firecloud.org/api-docs.yaml", # authenticate = FALSE # )) # } ## ----sessionInfo, echo=FALSE--------------------------------------------- # sessionInfo()