## ----include = FALSE----------------------------------------------------- has_gcloud <- AnVILBase::has_avworkspace( strict = TRUE, platform = AnVILGCP::gcp() ) knitr::opts_chunk$set( eval = has_gcloud, collapse = TRUE, cache = TRUE ) options(width=75) ## ----eval = FALSE-------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager", repos = "https://cran.r-project.org") # BiocManager::install("AnVIL") ## ----message =FALSE, eval = TRUE, cache = FALSE-------------------------- library(AnVILGCP) library(AnVIL) ## ----eval = FALSE-------------------------------------------------------- # dir(file.path(Sys.getenv("GCLOUD_SDK_PATH"), "bin"), "^(gcloud|gsutil)$") # ## [1] "gcloud" "gsutil" ## ----eval = TRUE--------------------------------------------------------- ## the code chunks in this vignette are fully evaluated when ## gcloud_exists() returns TRUE AnVILGCP::gcloud_exists() ## ----eval = FALSE-------------------------------------------------------- # BiocManager::install("GenomicFeatures") ## ----eval = FALSE-------------------------------------------------------- # add_libpaths("~/my/project") ## ----eval = has_gcloud--------------------------------------------------- # gcloud_account() # authentication account # gcloud_project() # billing project information ## ----eval = has_gcloud--------------------------------------------------- # gcloud_cmd("projects", "list") %>% # readr::read_table() %>% # filter(startsWith(PROJECT_ID, "anvil")) ## ----eval = FALSE-------------------------------------------------------- # gcloud_help("projects") ## ------------------------------------------------------------------------ # src <- "gs://genomics-public-data/1000-genomes/" ## ----eval = has_gcloud--------------------------------------------------- # 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) ## ----eval = has_gcloud--------------------------------------------------- # fl <- tempfile() # gsutil_cp(sample_info, fl) # # csv <- readr::read_csv(fl, guess_max = 5000L, col_types = readr::cols()) # csv ## ----eval = has_gcloud--------------------------------------------------- # pipe <- gsutil_pipe(fl, "rb") # readr::read_csv(pipe, guess_max = 5000L, col_types = readr::cols()) %>% # dplyr::select("Sample", "Family_ID", "Population", "Gender") ## ----eval = has_gcloud--------------------------------------------------- # 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, eval = has_gcloud------------------- # avworkspace_namespace("pathogen-genomic-surveillance") # avworkspace_name("COVID-19") ## ----eval = has_gcloud--------------------------------------------------- # avworkspace_namespace() # avworkspace_name() ## ----eval = has_gcloud--------------------------------------------------- # ## N.B.: IT MAY NOT BE NECESSARY TO SET THESE WHEN ON ANVIL # avworkspace_namespace("pathogen-genomic-surveillance") # avworkspace_name("COVID-19") ## ----eval = has_gcloud--------------------------------------------------- # avtables() # sample <- avtable("sample") # sample ## ----eval = has_gcloud--------------------------------------------------- # sample %>% # select("sample_id", contains("fasta")) %>% # filter(!is.na(final_assembly_fasta)) ## ----eval = FALSE-------------------------------------------------------- # my_cars <- # mtcars |> # as_tibble(rownames = "model") |> # mutate(model = gsub(" ", "_", model)) # job_status <- avtable_import(my_cars) ## ----eval = FALSE-------------------------------------------------------- # avtable_import_status(job_status) ## ----eval = FALSE-------------------------------------------------------- # (job_status <- avtable_import(my_cars, pageSize = 10)) # ## pageSize = 10 rows (4 pages) # ## |======================================================================| 100% # ## # A tibble: 4 × 5 # ## page from_row to_row job_id status # ## # ## 1 1 1 10 a32e9706-f63c-49ed-9620-b214746b9392 Uploaded # ## 2 2 11 20 f2910ac2-0954-4fb9-b36c-970845a266b7 Uploaded # ## 3 3 21 30 e18adc5b-d26f-4a8a-a0d7-a232e17ac8d2 Uploaded # ## 4 4 31 32 d14efb89-e2dd-4937-b80a-169520b5f563 Uploaded # (job_status <- avtable_import_status(job_status)) # ## checking status of 4 avtable import jobs # ## |======================================================================| 100% # ## # A tibble: 4 × 5 # ## page from_row to_row job_id status # ## # ## 1 1 1 10 a32e9706-f63c-49ed-9620-b214746b9392 Done # ## 2 2 11 20 f2910ac2-0954-4fb9-b36c-970845a266b7 Done # ## 3 3 21 30 e18adc5b-d26f-4a8a-a0d7-a232e17ac8d2 ReadyForUpsert # ## 4 4 31 32 d14efb89-e2dd-4937-b80a-169520b5f563 ReadyForUpsert # (job_status <- avtable_import_status(job_status)) # ## checking status of 4 avtable import jobs # ## |======================================================================| 100% # ## # A tibble: 4 × 5 # ## page from_row to_row job_id status # ## # ## 1 1 1 10 a32e9706-f63c-49ed-9620-b214746b9392 Done # ## 2 2 11 20 f2910ac2-0954-4fb9-b36c-970845a266b7 Done # ## 3 3 21 30 e18adc5b-d26f-4a8a-a0d7-a232e17ac8d2 Done # ## 4 4 31 32 d14efb89-e2dd-4937-b80a-169520b5f563 Done ## ----eval = FALSE-------------------------------------------------------- # ## editable copy of '1000G-high-coverage-2019' workspace # avworkspace("anvil-datastorage/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") ## ----eval = has_gcloud--------------------------------------------------- # avdata() ## ----eval = has_gcloud--------------------------------------------------- # bucket <- avbucket() # bucket ## ----eval = has_gcloud--------------------------------------------------- # 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")) ## ----eval = has_gcloud--------------------------------------------------- # 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 ## ----eval = has_gcloud--------------------------------------------------- # terra <- Terra() ## ----eval = has_gcloud--------------------------------------------------- # terra ## ----eval = has_gcloud--------------------------------------------------- # terra %>% tags("Status") ## ----eval = has_gcloud--------------------------------------------------- # terra$status # terra$status() ## ----eval = has_gcloud--------------------------------------------------- # args(terra$createBillingProjectFull) ## ----eval = has_gcloud--------------------------------------------------- # args(terra$overwriteWorkspaceMethodConfig) ## ----eval = has_gcloud--------------------------------------------------- # status <- terra$status() # class(status) ## ----eval = has_gcloud--------------------------------------------------- # str(status) ## ----eval = has_gcloud--------------------------------------------------- # lst <- status %>% as.list() # lengths(lst) # lengths(lst$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()