Compose BioCompute Object - Execution Domain (v1.3.0)

compose_execution_v1.3.0(
  script = NULL,
  script_driver = NULL,
  software_prerequisites = NULL,
  external_data_endpoints = NULL,
  environment_variables = NULL
)

compose_execution(
  script = NULL,
  script_driver = NULL,
  software_prerequisites = NULL,
  external_data_endpoints = NULL,
  environment_variables = NULL
)

Arguments

script

Character string. Points to internal or external references to an object that was used to perform computations for this BCO instance.

script_driver

Character string. Indicate what kind of executable can be launched in order to perform a sequence of commands described in the script in order to run the pipeline.

software_prerequisites

Data frame. The minimal necessary prerequisites, library, and tool versions needed to successfully run the script to produce BCO. Variables include name, version, uri, access_time, and sha1_chksum. Each row is one item in the output subdomain.

external_data_endpoints

Data frame. The minimal necessary domain-specific external data source access to successfully run the script to produce the BCO. Variables include mediatype, name, and url. Each row is one item in the output subdomain.

environment_variables

Data frame. Key-value pairs useful to configure the execution environment on the target platform. Variables include key and value.

Value

A list of class bco.domain

Examples

script <- "https://example.com/workflows/antiviral_resistance_detection_hive.py" script_driver <- "shell" software_prerequisites <- data.frame( "name" = c("HIVE-hexagon", "HIVE-heptagon"), "version" = c("babajanian.1", "albinoni.2"), "uri" = c( "https://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-", "https://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), "sha1_chksum" = c("d60f506cddac09e9e816531e7905ca1ca6641e3c", NA), stringsAsFactors = FALSE ) external_data_endpoints <- data.frame( "name" = c("generic name", "access to ftp server", "access to e-utils web service"), "url" = c( "protocol://domain:port/application/path", "ftp://data.example.com:21/", "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" ), stringsAsFactors = FALSE ) environment_variables <- data.frame( "key" = c("HOSTTYPE", "EDITOR"), "value" = c("x86_64-linux", "vim") ) compose_execution( script, script_driver, software_prerequisites, external_data_endpoints, environment_variables ) %>% convert_json()
#> { #> "script": "https://example.com/workflows/antiviral_resistance_detection_hive.py", #> "script_driver": "shell", #> "software_prerequisites": [ #> { #> "name": "HIVE-hexagon", #> "version": "babajanian.1", #> "uri": [ #> { #> "uri": "https://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-", #> "access_time": "2017-01-24 09:40:17", #> "sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c" #> } #> ] #> }, #> { #> "name": "HIVE-heptagon", #> "version": "albinoni.2", #> "uri": [ #> { #> "uri": "https://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-", #> "access_time": "2017-01-24 09:40:17", #> "sha1_chksum": "NA" #> } #> ] #> } #> ], #> "external_data_endpoints": [ #> [ #> { #> "name": "generic name", #> "url": "protocol://domain:port/application/path" #> } #> ], #> [ #> { #> "name": "access to ftp server", #> "url": "ftp://data.example.com:21/" #> } #> ], #> [ #> { #> "name": "access to e-utils web service", #> "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" #> } #> ] #> ], #> "environment_variables": { #> "HOSTTYPE": "x86_64-linux", #> "EDITOR": "vim" #> } #> }