Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
eval = FALSE
)
## -----------------------------------------------------------------------------
# # Install package from CRAN
# install.packages("sevenbridges2")
## -----------------------------------------------------------------------------
# # Install package from github
# remotes::install_github(
# "sbg/sevenbridges2",
# build_vignettes = TRUE, dependencies = TRUE
# )
## -----------------------------------------------------------------------------
# # Load the package
# library("sevenbridges2")
#
# # Authenticate
# a <- Auth$new(token = "<your_token>", platform = "aws-us")
#
# # List all projects with raw api() function
# a$api(path = "projects", method = "GET")
## -----------------------------------------------------------------------------
# # Create a collection of files
# public_files <- a$files$query(project = "admin/sbg-public-data")
#
# # Load next 50 results
# public_files$next_page()
#
# # Load previous 50 results
# public_files$prev_page()
#
# # Load all results
# public_files$all()
## -----------------------------------------------------------------------------
# # Create a collection of files
# public_files <- a$files$query(project = "admin/sbg-public-data")
#
# # Default print
# public_files
#
# # Print 20 items
# public_files$print(n = 20)
## -----------------------------------------------------------------------------
# # Search all public files
# public_files <- a$files$query(project = "admin/sbg-public-data")
#
# # Search files by name
# file_1000G_omni <- a$files$query(
# project = "admin/sbg-public-data",
# name = "1000G_omni2.5.b37.vcf"
# )
## -----------------------------------------------------------------------------
# # Search all public apps containing the STAR term
# public_star_apps <- a$apps$query(
# visibility = "public",
# query_terms = list("STAR")
# )
#
# # Search all projects that contain "demo" in the name
# demo_projs <- a$projects$query(name = "demo")
## -----------------------------------------------------------------------------
# # Load package
# library("sevenbridges2")
## -----------------------------------------------------------------------------
# # Authenticate with direct method
# a <- Auth$new(platform = "aws-us", token = "<your-token>")
## -----------------------------------------------------------------------------
# # Set environment variables
# sevenbridges2:::sbg_set_env(
# url = "https://api.sbgenomics.com/v2/",
# token = "<your_token>"
# )
## -----------------------------------------------------------------------------
# # Authenticate using environment variables
# a <- Auth$new(from = "env")
## -----------------------------------------------------------------------------
# # Load aws-us-<username> profile for authentication
# a <- Auth$new(
# from = "file",
# profile_name = "aws-us-<username>"
# )
## -----------------------------------------------------------------------------
# # Load default profile
# a <- Auth$new(from = "file")
## -----------------------------------------------------------------------------
# # Create Auth object with 'default' account
# a <- Auth$new(from = "file", profile_name = "default")
#
# # Create Auth object with 'aws-us-<username>' account
# b <- Auth$new(from = "file", profile_name = "aws-us-<username>")
## -----------------------------------------------------------------------------
# # Get currently authenticated user info
# a$user()
## -----------------------------------------------------------------------------
# # Get user info
# a$user(username = "<username>")
## -----------------------------------------------------------------------------
# # Get rate limit info
# a$rate_limit()
## -----------------------------------------------------------------------------
# # Check your billing info
# a$billing_groups$query()
## -----------------------------------------------------------------------------
# # Check your invoices
# a$invoices$query()
## -----------------------------------------------------------------------------
# # Get a single billing group
# a$billing_groups$get(id = "<billing_group_id>")
## -----------------------------------------------------------------------------
# # List first 5 projects
# my_projects <- a$projects$query(limit = 5)
# my_projects
#
# # Load next page of results
# my_projects$next_page()
#
# # Return all projects that contain the term "demo"
# demo_projects <- a$projects$query(name = "demo")
#
# # Return all projects tagged with "demo"
# tagged_projects <- a$projects$query(tags = list("demo"))
## -----------------------------------------------------------------------------
# # List all available billing groups for currently logged in user
# a$billing_groups$query()
#
# # Set the billing group for the new project
# bid <- "<billing_group_id>"
#
# # Create a new project
# p <- a$projects$create(
# name = "API testing", billing_group = bid,
# description = "This project has been created using the sevenbridges2 R API
# library."
# )
## -----------------------------------------------------------------------------
# # Get a single project by ID
# a$projects$get(id = "<your_username_or_division>/api-testing")
## -----------------------------------------------------------------------------
# # Search by name matching, with limit 10
# public_apps <- a$apps$query(
# visibility = "public",
# limit = 10,
# query_terms = list("STAR")
# )
#
# # Search by ID
# star_app <- a$apps$get(
# id = "admin/sbg-public-data/rna-seq-alignment-star/0"
# )
## -----------------------------------------------------------------------------
# # Copy app into the project
# a$apps$copy(
# app = star_app,
# project = "<username_or_division>/api-testing",
# name = "New copy of STAR"
# )
#
# # Check if it is copied
# p <- a$projects$get(id = "<username_or_division>/api-testing")
#
# # List the apps you have in your project
# p$list_apps()
## -----------------------------------------------------------------------------
# # Get public app RNA Sequencing alignment - STAR
# star_app <- a$apps$get(
# id = "admin/sbg-public-data/rna-seq-alignment-star/0"
# )
#
# # Copy it into a project
# star_app$copy(
# project = "<username_or_division>/api-testing",
# name = "Copy of STAR"
# )
## -----------------------------------------------------------------------------
# # Fetch copied app
# copied_star_app <- a$apps$get(
# id = "<username_or_division>/api-testing/newcopyofstar/0"
# )
#
# # Preview its inputs
# copied_star_app$input_matrix()
## -----------------------------------------------------------------------------
# # Get reads (fastq) files and and copy them into a project
# reads_1 <- a$files$get(id = "641c48c425ed1842bd0bf799") # file id
# reads_1$copy_to(project = p)
#
# reads_2 <- a$files$get(id = "641c48c425ed1842bd0bf835") # file id
# reads_2$copy_to(project = p)
#
# # Get a single file reference file and copy into a project
# fasta_in <- a$files$get(id = "641c48c525ed1842bd0bf86a") # file id
# fasta_in$copy_to(project = p)
#
# # Get gtf file and copy into a project
# gtf_in <- a$files$get(id = "641c48c425ed1842bd0bf825") # file id
# gtf_in$copy_to(project = p)
#
# # Get copied files
# input_files <- p$list_files()$items
## -----------------------------------------------------------------------------
# # Add new tasks
# taskName <- paste0("STAR-alignment ", date())
#
# tsk <- p$create_task(
# name = taskName,
# description = "STAR test",
# app = copied_star_app,
# inputs = list(
# "fastq" = c(input_files[[1]], input_files[[2]]),
# "genomeFastaFiles" = input_files[[3]],
# "sjdbGTFfile" = list(input_files[[4]])
# )
# )
#
# # Preview task
# tsk$print()
## -----------------------------------------------------------------------------
# # Get app's outputs details
# copied_star_app$output_matrix()
## -----------------------------------------------------------------------------
# # Run your task
# tsk$run()
## -----------------------------------------------------------------------------
# # Update task
# tsk$update(description = "New RNA SEQ Alignment - STAR task")
## -----------------------------------------------------------------------------
# # Reload task
# tsk$reload()
# tsk$status
## -----------------------------------------------------------------------------
# # Abort your task
# tsk$abort()
## -----------------------------------------------------------------------------
# # Rerun your task
# tsk$rerun()
## -----------------------------------------------------------------------------
# # First clone existing task
# cloned_task <- tsk$clone_task()
#
# # Then, update GTF input file in the cloned task
# cloned_task$update(inputs = list(sjdbGTFfile = "<some new file>"))
# cloned_task$run()
## -----------------------------------------------------------------------------
# # # not run
# # tsk$delete()
## -----------------------------------------------------------------------------
# # Create project with disabled spot instances
# p <- a$projects$create(
# name = "spot-disabled-project", bid, description = "spot disabled project",
# use_interruptible = FALSE
# )
## -----------------------------------------------------------------------------
# # Create task and set usage of interruptible instances to TRUE
# tsk <- p$create_task(
# name = paste0("spot enabled task in a spot disabled project"),
# description = "spot enabled task",
# app = copied_star_app,
# inputs = list(
# "fastq" = c(input_files[[1]], input_files[[2]]),
# "genomeFastaFiles" = input_files[[3]],
# "sjdbGTFfile" = list(input_files[[4]])
# ),
# use_interruptible_instances = TRUE
# )
## -----------------------------------------------------------------------------
# # Create task with setting instance type and number of parallel instances
# tsk <- p$create_task(
# ...,
# execution_settings = list(
# instance_type = "c4.2xlarge;ebs-gp2;2000",
# max_parallel_instances = 2
# )
# )
## -----------------------------------------------------------------------------
# # Add two more fastq files that will be used in our task inputs
# # and copy them into our API testing project
# reads_3 <- a$files$get(id = "641c48c425ed1842bd0bf7b6") # file id
# reads_3$copy_to(project = p)
#
# reads_4 <- a$files$get(id = "641c48c425ed1842bd0bf7a5") # file id
# reads_4$copy_to(project = p)
#
# # Get all project files
# input_files <- p$list_files()$items
#
# taskName <- paste0("STAR-alignment ", date())
#
# # Create task with batch criteria
# tsk <- p$create_task(
# name = taskName,
# description = "Batch Star Test",
# app = copied_star_app,
# batch = TRUE,
# batch_input = "fastq",
# batch_by = list(
# type = "CRITERIA",
# criteria = list("metadata.sample_id")
# ),
# inputs = list(
# "fastq" = c(
# input_files[[1]],
# input_files[[2]],
# input_files[[3]],
# input_files[[4]]
# ),
# "genomeFastaFiles" = input_files[[5]],
# "sjdbGTFfile" = list(input_files[[6]])
# )
# )
#
# # Run batch task
# tsk$run()
## -----------------------------------------------------------------------------
# # List parent task children and their execution details
# child_tasks <- tsk$list_batch_children()
#
# child1_details <- child_tasks$items[[1]]$get_execution_details()
# child2_details <- child_tasks$items[[2]]$get_execution_details()
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