## ----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--------------------------------------------------------
# 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
# ## <int> <int> <int> <chr> <chr>
# ## 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
# ## <int> <int> <int> <chr> <chr>
# ## 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
# ## <int> <int> <int> <chr> <chr>
# ## 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("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://<avbucket()>/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
# ## <chr> <chr> <dbl> <chr> <chr> <chr> <list> <chr> <chr>
# ## 1 drs://d… NA21144… 7.06e9 gs:/… NA 2020-07-08… <named list> fc-56… CCDG…
# ## 2 drs://d… NA21144… 4.08e6 gs:/… NA 2020-07-08… <named list> 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()