List all API paths
This call returns all API paths, so that you don't need to rely on documentation in the terminal.
https://api.sbgenomics.com/v2/https://eu-api.sbgenomics.com/v2/https://gcp-api.sbgenomics.com/v2/Listing API calls
Your authentication token is not necessary to make this call (only).
GET /v2/ HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET https://api.sbgenomics.com/v2/{
"rate_limit_url": "https://api.sbgenomics.com/v2/rate_limit",
"user_url": "https://api.sbgenomics.com/v2/user",
"users_url": "https://api.sbgenomics.com/v2/users",
"billing_url": "https://api.sbgenomics.com/v2/billing",
"projects_url": "https://api.sbgenomics.com/v2/projects",
"files_url": "https://api.sbgenomics.com/v2/files",
"tasks_url": "https://api.sbgenomics.com/v2/tasks",
"apps_url": "https://api.sbgenomics.com/v2/apps",
"action_url": "https://api.sbgenomics.com/v2/action",
"upload_url":"https://api.sbgenomics.com/v2/upload",
"storage_url": "https://api.sbgenomics.com/v2/storage"
}
Get my information
For general information on the API, including formatting, parameters, and pagination, please see the API Overview.
This call returns information about your account on the Seven Bridges Platform.
https://api.sbgenomics.com/v2/userhttps://eu-api.sbgenomics.com/v2/userhttps://gcp-api.sbgenomics.com/v2/userX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
fields
string
Selector specifying a subset of fields to include in the response.
In the response body, you can see the information about your account. If you have associated a CGC account with your Seven Bridges Platform account, you can see the type of TCGA data you can access under tags, such as tcga-oa for TCGA Open Data and tcga-ca for TCGA Controlled Data.
GET /v2/user HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://cgc-api.sbgenomics.com/v2/user"{
"href": "https://api.sbgenomics.com/v2/users/RFranklin",
"username": "RFranklin",
"email": "[email protected]",
"first_name": "Rosalind",
"last_name": "Franklin",
"tags": [
{
"tag": "tcga-oa",
"expires_at": 3053937952000
},
{
"tag": "tcga-ca",
"expires_at": 1506729600000
}
],
"affiliation": "Seven Bridges",
"phone": "",
"address": "",
"city": "London",
"state": "",
"country": "United Kingdom",
"zip_code": ""
}List user resources
This call returns information about the specified user. Note that currently you can view only your own user information, and so this call is equivalent to the call to Get my information.
https://api.sbgenomics.com/v2/users/{username}https://eu-api.sbgenomics.com/v2/users/{username}https://gcp-api.sbgenomics.com/v2/users/{username}This call will only return a successful response if {username} is replaced with your own username.
Case sensitivity
Don't forget to capitalize your username in the same way as you set it when you registered on the Seven Bridges Platform.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
username
Username of the user you are querying.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/users/RFranklin HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/users/RFranklin"{
"href": "https://api.sbgenomics.com/v2/users/RFranklin",
"username": "RFranklin",
"email": "[email protected]",
"first_name": "Rosalind",
"last_name": "Franklin",
"affiliation": "Seven Bridges",
"phone": "",
"address": "",
"city": "London",
"state": "",
"country": "United Kingdom",
"zip_code": ""
}List billing API paths
This call returns a list of paths used to access billing information via the API.
https://api.sbgenomics.com/v2/billinghttps://eu-api.sbgenomics.com/v2/billinghttps://gcp-api.sbgenomics.com/v2/billingX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/billing HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: a42c0608d5934bdeb91d0f9e0cdddb48curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/billing"{
"billing_groups_url": "https://api.sbgenomics.com/v2/billing/groups/",
"invoices_url": "https://api.sbgenomics.com/v2/billing/invoices/"
}List billing groups
This call lists all your billing groups, including groups that are pending or have been disabled.
https://api.sbgenomics.com/v2/billing/groups https://eu-api.sbgenomics.com/v2/billing/groups https://gcp-api.sbgenomics.com/v2/billing/groupsX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
fields
string
Selector specifying a subset of fields to include in the response.
limit
integer
The maximum number of collection items to return for a single request. Minimum value is 1. The maximum value is 100 and the default value is 25. This is a pagination-specific attribute.
offset
integer
The zero-based starting index in the entire collection of the first item to return. The default value is 0. This is a pagination-specific attribute.
GET /v2/billing/groups HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" GET "https://api.sbgenomics.com/v2/billing/groups"{
"href": "https://api.sbgenomics.com/v2/billing/groups?offset=0&limit=25",
"items": [
{
"id": "eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7",
"href": "https://api.sbgenomics.com/v2/billing/groups/eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7",
"name": "RFranklin Billing Group"
}
],
"links": []
}Get a single billing group
This call retrieves a single billing group, specified by {billing_group}. To find the billing_group, use the call list billing groups to list all your billing groups. The information returned includes the billing group owner, the total balance, and the status of the billing group (pending or confirmed).
https://api.sbgenomics.com/v2/billing/groups/{billing_group}https://eu-api.sbgenomics.com/v2/billing/groups/{billing_group}https://gcp-api.sbgenomics.com/v2/billing/groups/{billing_group}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
billing_group
required
ID of the billing group you are querying.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/billing/groups/8ccc6222-ef6f-4526-99d7-9f56b716d43a HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 97a1ad73db6349a487ef77b7655edae2curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/billing/groups/eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7"{
{
"id": "eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7",
"href": "https://api.sbgenomics.com/v2/billing/groups/eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7",
"owner": "RFranklin",
"name": "RFranklin Billing Group",
"type": "free",
"pending": false,
"disabled": false,
"balance": {
"currency": "USD",
"amount": 0
}
}Get breakdown for a billing group
This call returns a breakdown of spending per-project for the billing group specified by billing_group. For each project that the billing group is associated with, information is shown on each task run, including its initiating user (the runner_username), start and end times, and cost.
To find the billing_group, use the call list billing groups to list all your billing groups.
https://api.sbgenomics.com/v2/billing/groups/{billing_group}/breakdownhttps://eu-api.sbgenomics.com/v2/billing/groups/{billing_group}/breakdownhttps://gcp-api.sbgenomics.com/v2/billing/groups/{billing_group}/breakdownBilling periods
The spending will be shown for the current billing period.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
billing_group
The ID of the billing group.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/billing/groups/8ccc6222-ef6f-4526-99d7-9f56b716d43a/breakdown HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 8ccc6222-ef6f-4526-99d7-9f56b716d43a" -H "content-type: application/json" - X GET "https://api.sbgenomics.com/v2/billing/groups/eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7/breakdown"{
"href": "https://api.sbgenomics.com/v2/billing/groups/eb5fdee2-36c3-41d1-b179-d9f5d0a0f6f7/breakdown",
"project_breakdown": [
{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/my_project",
"analysis_spending": {
"currency": "USD",
"amount": "0.23"
},
"task_breakdown": [
{
"href": "https://api.sbgenomics.com/v2/tasks/39bc3e8c-6cf6-4f8f-b550-21e9633c1f4b",
"runner_username": "Kate",
"time_started": "2015-12-11T11:03:08Z",
"time_finished": "2015-12-11T11:08:49Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
}
]
},
{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/test",
"analysis_spending": {
"currency": "USD",
"amount": "0.92"
},
"task_breakdown": [
{
"href": "https://api.sbgenomics.com/v2/tasks/f586a3fb-c9e4-4415-b22b-648a66969a37",
"runner_username": "RFranklin",
"time_started": "2015-11-26T14:15:18Z",
"time_finished": "2015-11-26T14:20:30Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
{
"href": "https://api.sbgenomics.com/v2/tasks/98c8dc8b-e1e0-4410-8448-d857a9c2cf16",
"runner_username": "RFranklin",
"time_started": "2015-11-25T16:26:23Z",
"time_finished": "2015-11-25T16:30:46Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
{
"href": "https://api.sbgenomics.com/v2/tasks/6961273b-0f6a-45a3-95c1-d5d895fc6ea0",
"runner_username": "RFranklin",
"time_started": "2015-11-26T12:11:58Z",
"time_finished": "2015-11-26T12:16:33Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
]
},
{
"href": "https://api.sbgenomics.com/v2/projects/Kate/my-project",
"analysis_spending": {
"currency": "USD",
"amount": "0.46"
},
"task_breakdown": [
{
"href": "https://api.sbgenomics.com/v2/tasks/a466e8b9-6f48-4cf9-b903-50fc4701bb2e",
"runner_username": "RFranklin",
"time_started": "2015-11-25T14:02:13Z",
"time_finished": "2015-11-25T14:07:06Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
{
"href": "https://api.sbgenomics.com/v2/tasks/b0bbeda6-153b-4801-92ad-82bc0e58bdb6",
"runner_username": "RFranklin",
"time_started": "2015-11-24T19:19:52Z",
"time_finished": "2015-11-24T19:24:45Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
]
},
{
"analysis_spending": {
"currency": "USD",
"amount": "0.69"
},
"task_breakdown": [
{
"href": "https://api.sbgenomics.com/v2/tasks/468dca93-7e90-4625-bcef-a080151d0687",
"runner_username": "RFranklin",
"time_started": "2015-11-25T14:30:45Z",
"time_finished": "2015-11-25T14:35:31Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
{
"href": "https://api.sbgenomics.com/v2/tasks/dc0e6559-a706-4e30-a040-72e5bfb3c077",
"runner_username": "RFranklin",
"time_started": "2015-11-25T14:37:59Z",
"time_finished": "2015-11-25T14:47:10Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
},
{
"href": "https://api.sbgenomics.com/v2/tasks/a8364b07-f1f9-4548-864a-045a3a2c41a1",
"runner_username": "RFranklin",
"time_started": "2015-11-25T14:43:02Z",
"time_finished": "2015-11-25T14:48:18Z",
"task_cost": {
"currency": "USD",
"amount": "0.23"
}
}
]
}
],
"total_spending": {
"currency": "USD",
"amount": "2.00"
}
}List invoices
This call returns a list of invoices, with information about each, including whether or not the invoice is pending and the billing period it covers.
The call returns information about all your available invoices, unless you use the query parameter bg_id to specify the ID of a particular billing group, in which case it will return the invoice incurred by that billing group only.
https://api.sbgenomics.com/v2/billing/invoiceshttps://eu-api.sbgenomics.com/v2/billing/invoiceshttps://gcp-api.sbgenomics.com/v2/billing/invoicesX-SBG-Auth-Token
required
Your Platform authentication token.
fields
string
Selector specifying a subset of fields to include in the response.
GET v2/billing/invoices HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET https://api.sbgenomics.com/v2/billing/invoices -H "Accept: application/json"{
"href": "https://api.sbgenomics.com/v2/billing/invoices/",
"items": [
{
"href": "https://api.sbgenomics.com/v2/billing/invoices/7779079019",
"invoice_id": "7779079019",
"pending": false,
"invoice_period": {
"from": "2015-03-26T13:55:26Z",
"to": "2015-03-27T00:00:00Z"
}
},
{
"href": "https://api.sbgenomics.com/v2/billing/invoices/7443918961",
"invoice_id": "7443918961",
"pending": false,
"invoice_period": {
"from": "2015-03-27T00:00:00Z",
"to": "2015-03-30T00:00:00Z"
}
}
]
}Get a specific invoice
This call retrieves information about a selected invoice, including the costs for analysis and storage, and the invoice period.
Use the call to list invoices to retrieve the invoice_ids for a specified billing group.
https://api.sbgenomics.com/v2/billing/invoices/{invoice_id}https://eu-api.sbgenomics.com/v2/billing/invoices/{invoice_id}https://gcp-api.sbgenomics.com/v2/billing/invoices/{invoice_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
invoice_id
The ID of the invoice you are querying.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/billing/invoices/7779079019 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/billing/invoices/7779079019"{
"href": "https://api.sbgenomics.com/v2/billing/invoices/7779079019",
"invoice_id": "7779079019",
"pending": false,
"approval_date": "2015-03-26T00:00:00Z",
"invoice_period": {
"from": "2015-03-26T13:55:26Z",
"to": "2015-03-27T00:00:00Z"
},
"analysis_costs": {
"currency": "USD",
"amount": "1.64"
},
"storage_costs": {
"currency": "USD",
"amount": "0.00"
},
"total": {
"currency": "USD",
"amount": "1.64"
}
}List all your projects
This call returns a list of all projects you are a member of. Each project's project_id and URL on the Seven Bridges Platform will be returned.
https://api.sbgenomics.com/v2/projectshttps://eu-api.sbgenomics.com/v2/projectshttps://gcp-api.sbgenomics.com/v2/projectsX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
name
string
Filter projects by the project name. The search is partial and case-insensitive.
offset
integer
The zero-based starting index in the entire collection of the first item to return. The default value is 0. This is a pagination-specific attribute.
limit
integer
The maximum number of collection items to return for a single request. Minimum value is 1. The maximum value is 100 and the default value is 25. This is a pagination-specific attribute.
fields
fields
Selector specifying a subset of fields to include in the response.
GET /v2/projects HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/projects"{
"href": "https://api.sbgenomics.com/v2/projects?offset=0&limit=25",
"items": [
{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/test",
"id": "RFranklin/test",
"name": "test"
"created_by": "rfranklin",
"created_on": "2019-04-24T11:51:20Z",
"modified_on": "2019-04-24T11:51:20Z"
},
{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/sandbox",
"id": "RFranklin/sandbox",
"name": "sandbox"
"created_by": "rfranklin",
"created_on": "2019-04-24T11:51:20Z",
"modified_on": "2019-04-24T11:51:20Z"
},
{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/my-project",
"id": "RFranklin/my-project",
"name": "my project"
"created_by": "rfranklin",
"created_on": "2019-04-24T11:51:20Z",
"modified_on": "2019-04-24T11:51:20Z"
}
],
"links": []
}List projects owned by a particular user
List the projects owned by and accessible to a particular user. Each project's ID and URL will be returned. Please keep in mind that you will only be able to list projects you are a member of.
https://api.sbgenomics.com/v2/projects/{owner}https://eu-api.sbgenomics.com/v2/projects/{owner}https://gcp-api.sbgenomics.com/v2/projects/{owner}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
owner
The owner whose projects you want to query.
name
string
Filter projects by the project name. The search is partial and case-insensitive.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/projects/rfranklin HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/projects/RFranklin"{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin",
"items": [
{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/Quickstart",
"id": "rfranklin/Quickstart",
"name": "Quickstart",
"created_by": "rfranklin",
"created_on": "2017-07-18T11:19:48Z",
"modified_on": "2017-07-18T11:19:48Z"
},
{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/my-project",
"id": "rfranklin/my-project",
"name": "My project",
"description": "testing testing.\n* one\n* two\n* three"
"created_by": "rfranklin",
"created_on": "2017-07-18T11:19:48Z",
"modified_on": "2017-07-18T11:19:48Z"
}
]
}Create a new project
This call creates a new project.
https://api.sbgenomics.com/v2/projectshttps://eu-api.sbgenomics.com/v2/projectshttps://gcp-api.sbgenomics.com/v2/projectsX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
fields
string
Selector specifying a subset of fields to include in the response.
Request body
In the body, you should enter a list of key-value pairs. The keys, and the values they take, are described in the following table.
name
required
string
The name of the project you are creating.
description
string
A description of the project.
billing_group
required
string
The ID of the billing group for the project.
List all billing groups to find your billing group ID
settings
dictionary
This dictionary contains two fields, locked and use_interruptible_instances - see below for further information.
locked
boolean
This field can be true or false.
Set this field to true to lock down a project. Locking down a project prevents any Seven Bridges team member from viewing any information about the task.
controlled
boolean
This field can be true or false.
Set this field to true to define this project as controlled i.e. one which will contain controlled data.
Set false to define the project as open i.e. one which will contain open data.
location
boolean
Use this field to specify the location for this project:
aws:us-east-1aws:us-west-2
use_interruptible_instances
boolean
This field can be true or false. If not included in the request, spot instances are enabled by default.
intermediate_files
dictionary
Specifies intermediate files retention period.
To do this, specify a dictionary with the following format:
{ "retention": "LIMITED",
"duration": 24 }
The minimum value is 1 h. The maximum value is 120 h and the default value is 24 h.
Project short names
Recall from the API Overview that projects are assigned short names. When you specify the given name of your project, in the request body, the short name will be automatically generated, using the process described in the API Overview.
POST /v2/projects HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
content-type: application/json
curl --data '{"name": "My New Project", "description": "A project for testing my apps", "billing_group": "1f0c2751-694c-4e98-b863-06b68f5a61ca"}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/projects"{
"name": "My new project",
"description": "This is my new project",
"billing_group": "e291343d-032e9-43283-917a-898fba99dca0",
"settings":{
"locked": false,
"controlled": true,
"location": "aws:us-west-2",
"use_interruptible_instances": false,
"use_memoization": true,
"intermediate_files": {
"retention":"LIMITED",
"duration":24
}
}
}{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/my-new-project",
"id": "rfranklin/my-new-project",
"name": "My new project",
"type": "v2",
"description": "This is my new project",
"tags": [],
"settings": {
"locked": false,
"controlled": true,
"location": "aws:us-west-2",
"use_interruptible_instances": false,
"use_memoization": true,
"intermediate_files": {
"duration": 24,
"retention": "LIMITED"
}
},
"root_folder": "5d8cae1be4b0cbef3002f893",
"billing_group": "e291343d-02e9-4283-915a-898fba99dca0"
}Interpreting the response body
- The response will include an empty list
[]for the objecttags. This is a legacy feature of the API, and should be ignored. - The field
lockedis set totrue, which means you've created a locked project. Locking down a project prevents any Seven Bridges team member from viewing any information about the task.
Edit a project
This call edits a project on the Seven Bridges Platform. As a project Admin you can use it to change the name, settings, or billing group of the project.
Users with write permissions in the project can change the project description.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}https://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}https://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}PATCH
If your client does not support PATCH requests, you can use POST to send this request, along with the query parameter _method=PATCH:
i.e. https://api.sbgenomics.com/v2/projects/{project_owner}/{project}?_method=PATCH
Referring to your project
Note that project_owner is always case-sensitive, and that project is not the project's name but its ID, or short name. For full details of identifying objects using the API, please see the API overview.
Request body
The request body should contain a set of key-value pairs. The keys, and the values they take, are described in the following table. Enter a key-value pair if you want to re-set the existing value for the project.
Note that although you may change the name of the project, this does not affect its short name, which is immutable.
name
string
The name of the project you are editing.
billing_group
string
The ID of the billing group for the project.
List all billing groups to find your billing group ID.
settings
dictionary
This dictionary contains the following keys:
lockeduse_interruptible_instances.use_memoizationintermediate_files
locked
Boolean
This field can be true or false.
Set this field to true to lock down a project. Locking down a project prevents any Seven Bridges team member from viewing any information about the project.
use_interruptible_instances
Boolean
This field can be true or false to enable or disable the use of spot instances.
intermediate_files
dictionary
Specifies intermediate filesretention period.
To do this, specify a dictionary with the following format:
{ "retention": "LIMITED",
"duration": 24 }
The minimum value is 1 h. The maximum value is 120 h and the default value is 24 h.
description
string
A description of the project.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The short name of the project you are editing.
project_owner
The owner of the project you are editing.
fields
string
Selector specifying a subset of fields to include in the response.
PATCH /v2/projects/RFranklin/sandbox HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl --data '{"name": "New name for my project", "description": "Updated with the results of the latest experiments"}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X PATCH "https://api.sbgenomics.com/v2/projects/RFranklin/sandbox"{
"name": "my project",
"description": "Updated with the results of the latest experiments",
"settings": {
"locked": true,
"use_interruptible_instances": false,
"use_memoization": true,
"intermediate_files": {
"retention":"LIMITED",
"duration":24
}
}
}{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/project-via-api",
"id": "rfranklin/project-via-api",
"name": "my project",
"type": "v2",
"description": "Updated with the results of the latest experiments",
"tags": [],
"settings": {
"locked": true,
"controlled": false,
"location": "aws:us-east-1",
"use_interruptible_instances": false,
"use_memoization": true,
"intermediate_files": {
"duration": 24,
"retention": "LIMITED"
}
},
"permissions": {
"write": true,
"read": true,
"copy": true,
"execute": true,
"admin": true
},
"root_folder": "595b8ca0e4b0a50d07cb58f9",
"billing_group": "2791e8dc-4bb0-4314-9f3a-a8113e21e58c",
"created_by": "rfranklin",
"created_on": "2017-07-04T12:40:00Z",
"modified_on": "2019-05-20T12:49:34Z"
}Get details of a project
This call returns the details of a specified project.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}https://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}https://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}Referring to your project
Note that project_owner is always case-sensitive, and that project is not the project's name but its short name. For full details of identifying objects using the API, please see the API overview.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The short name of the project you are querying.
project_owner
The owner of the project you are querying.
fields
string
Selector specifying a subset of fields to include in the response.
Set this to _all to view all fields, including project settings.
This example response body displays the JSON returned when the fields parameter in the request is set to _all.
GET /v2/projects/rfranklin/my-project HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/projects/RFranklinate/my-project"{
"href": "http://api.sbgenomics.com/v2/projects/rfranklin/rfranklin-s-demo-project",
"id": "rfranklin/rfranklin-s-demo-project",
"name": "rfranklin's Demo Project",
"type": "v2",
"description": "This project contains data, completed analyses, and results.\n\Contains WGS, WES, and two different RNA-Seq read alignments - STAR and TopHat, fusion transcript detection analysis using ChimeraScan, FASTQ quality control and more.\n\n Open it up and take a look.",
"tags": [],
"settings": {
"locked": false,
"use_interruptible_instances": false,
"use_memoization": true,
"intermediate_files": {
"retention":"LIMITED",
"duration":24
}
},
"permissions": {
"write": true,
"read": true,
"copy": true,
"execute": true,
"admin": true
},
"root_folder": "595b8ca0e4b0a50d07cb58f9",
"billing_group": "2791e8dc-4bb0-4314-9f3a-a8113e21e58c",
"created_by": "rfranklin",
"created_on": "2017-07-04T12:40:00Z",
"modified_on": "2019-05-20T12:49:34Z"
}Interpreting the response body
- The object
typein the response should be ignored: all projects have typev2. - The dictionary
settingscontains one Boolean field,locked. This field shows whether or not your project is locked. You can lock down a project to prevent any Seven Bridges team member from viewing information about your project. Learn more about creating a locked project.
Delete a project
This call deletes a project from the Seven Bridges Platform. It can only be successfully made if you have admin status for the project.
Warning
Deleting a project completely erases the project and any of its related data from the Seven Bridges Platform.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}https://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}https://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}Referring to your project
Note that project_owner is always case-sensitive, and project is not the project's name but its short name. For full details of identifying objects using the API, please see the API Overview
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The short name of the project you are deleting.
project_owner
The owner of the project you are deleting.
DELETE /v2/projects/RFranklin/my-project HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X DELETE -H "X-SBG-Auth-Token: ce7ae5ab85e946599298e88a3430fba0" 'http://api.sbgenomics.com//v2/projects/RFranklin/my-project'List members of a project
This call returns a list of the members of the specified project. For each member, the response lists:
- The member's username on the Seven Bridges Platform
- The member's permissions in the project specified
Project member permissions
For information about the permissions project members may have, see the documentation on setting permissions.
https://api.sbgenomics.com/v2/projects/{owner}/{project}/membershttps://eu-api.sbgenomics.com/v2/projects/{owner}/{id}/membershttps://gcp-api.sbgenomics.com/v2/projects/{owner}/{project}/membersX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The ID of the project you are querying.
owner
The owner of the project you are querying.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/projects/rfranklin/my-project/members HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/projects/RFranklin/my-project/members"{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/project-via-api/members?offset=0&limit=50",
"items": [
{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/project-via-api/members/gazibara",
"id": "rfranklin",
"username": "rfranklin",
"email": "[email protected]",
"type": "USER",
"permissions": {
"write": true,
"read": true,
"copy": true,
"execute": true,
"admin": true
}
},
{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/project-via-api/members/john.smith",
"id": "john.smith",
"username": "john.smith",
"email": "[email protected]",
"type": "USER",
"permissions": {
"write": true,
"read": true,
"copy": true,
"execute": true,
"admin": false
}
},
{
"href": "https://api.sbgenomics.com/v2/projects/rfranklin/project-via-api/members/francis.crick",
"id": "fcrick",
"username": "fcrick",
"email": "[email protected]",
"type": "USER",
"permissions": {
"write": true,
"read": true,
"copy": true,
"execute": true,
"admin": false
}
}
],
"links": []
}Add a member to a project
This call adds a new user to a specified project. It can only be successfully made by a user who has admin permissions in the project.
Users may have the following permissions on the Platform:
- Read
- Write
- Copy
- Execute
- Admin
For more information, see the documentation on setting project member permissions. Note that some user permissions imply others: for example, if you give a user admin permission, then they automatically receive read, write, copy and execute permissions.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}/membershttps://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}/membershttps://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}/membersMember permissions
Requests to add a project member must include the key permissions. However, if you do not include a value for some permission, it will be set to false by default. The exception to this rule is the read permission, which is the default permission on a project. It enables a user to read project data, including file names, but access file contents.
For more information, see the documentation on setting permissions.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The ID of the project you are adding someone to.
project_owner
The owner of the project you are adding someone to.
fields
string
Selector specifying a subset of fields to include in the response.
Request body
Inside the body of the call you should enter a set of key-value pairs. The following table describes the values you should enter.
username
string
The Seven Bridges Platform username of the person you want to add to the project.
You should use either 'username' (recommended) or 'email'.
email
string
The email address of the person you want to add to the project.
This has to be the email address that the person used when registering for an account on the Seven Bridges Platform.
You should use either 'username' (recommended) or 'email'.
permissions
array of key-value pairs. The keys are strings, and the values are Booleans.
The possible keys are:
"write"
"read"
"copy"
"execute"
"admin"
Each key may have the values true or false.
Read permissions
All members of a project have read permissions by default. Even if you try setting read permissions to false, they will still default to true.
POST /v2/projects/rjfranklin/my-project/members HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl --data '{"username": "Jane-Doe", "permissions": { "read": true, "write": true, "execute": false}}' -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/projects/RFranklin/my-project/members"{
"username" : "Jane_Doe",
"permissions": {
"read" : true,
"write": true,
"execute": false
}
}{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/my-project/members/Jane_Doe",
"username": "Jane_Doe",
"email: "jane_doe@address.com",
"permissions": {
"write": true,
"read": true,
"copy": false,
"execute": true,
"admin": false
}
}Remove a project member
This call removes a project member from a project. It can only be successfully run by a user who has admin privileges in the project.
For more information on permissions on the Seven Bridges Platform, see the documentation on setting permissions.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}https://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}https://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project_owner
required
The Seven Bridges Platform username of the user who owns the project.
project
required
The ID of the project to access.
username
required
The Seven Bridges Platform username of the user you are removing.
DELETE /v2/projects/rfranklin/my-project/members/jane_doe HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X DELETE "https://api.sbgenomics.com/v2/projects/RFranklin/my-project/members/Jane_Doe" Get a project member's permissions
This returns the permissions of a specified user within a specified project.
Users may have the following permissions on the Seven Bridges Platform:
- Read
- Write
- Copy
- Execute
- Admin
Permissions are granted at the project-level. You may, for instance, have admin permission in one project, execute permission in another, and read-only permission in a third.
For more information on permissions on the Seven Bridges Platform, see the documentation on setting permissions.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}https://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}https://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project_owner
required
The Seven Bridges Platform username of the user who owns the project.
project
required
The short name of the project to access.
username
required
The Seven Bridges Platform username of the user whose permissions you are enquiring about.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/projects/rfranklin/my-project/members/jane_doe HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/projects/RFranklin/my-project/members/Jane_Doe"{
"href": "https://api.sbgenomics.com/v2/projects/RFranklin/my-project1/members/Jane_Doe",
"username": "Jane_Doe",
"email: "janedoe@address.com",
"permissions": {
"write": true,
"read": true,
"copy": false,
"execute": true,
"admin": false
}
}Modify a project member's permissions
This call edits a user's permissions in a specified project. It can only be successfully made by a user who has admin permissions in the project.
PUT and PATCH
The Seven Bridges Platform API has two method to modify project members' permissions. This method uses the HTTP verb PATCH, and the other uses the HTTP verb PUT.
The difference between the two concerns the way that they update the information stored about the user. PATCH allows you to update just one part of the user's information --- for instance, just the value stored for the user's copy permission. On the other hand, a PUT request will fully overwrite the user's permission information. This means that when issuing a PUT request you must enter values for every key required to describe the user, even if the values for some keys are unchanged.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{member}/permissionshttps://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{member}/permissionshttps://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{member}/permissionsX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The short name of the project containing the project member.
project_owner
The owner of the project containing the project member.
member
The project member whose permissions you are editing.
fields
string
Selector specifying a subset of fields to include in the response.
Request body
Inside the body of the call you should enter a set of key-value pairs. The following table describes the values you should enter.
read
Boolean: true or false
User can view file names, metadata, and workflows. They cannot view file contents.
All members of a project have read permissions by default. Even if you try setting read permissions to false, they will still default to true.
write
Boolean: true or false
User can add, modify, and remove files and workflows in a project.
Set value to true to assign the user write permission. Set to false to remove write permission.
copy
Boolean: true or false
User can view file content, copy, and download files from a project.
Set value to true to assign the user copy permission. Set to false to remove copy permission.
execute
Boolean: true or false
User can execute workflows and abort tasks in a project.
Set value to true to assign the user execute permission. Set to false to remove execute permission.
admin
Boolean: true or false
User can modify another user's permissions on a project, add or remove people from the project and manage funding sources. They also have all of the above permissions.
Set value to true to assign the user admin permission. Set to false to remove admin permission.
PATCH /v2/projects/RFranklin/test/members/crick/permissions HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl --data '{"write": true}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X PATCH "https://api.sbgenomics.com/v2/projects/RFranklin/test/members/crick/permissions" {
"write": true,
}{
"write": true,
"read": true,
"copy": false,
"execute": false,
"admin": false
}Overwrite a project member's permissions
This call changes a project member's permissions for a specified project.
Users may have the following permissions on the Seven Bridges Platform:
- Read
- Write
- Copy
- Execute
- Admin
For more information, see the documentation on setting project member permissions. Note that some user permissions imply others: for example, if you give a user admin permission, then they automatically receive read, write, copy and execute permissions.
PUT and PATCH
The Seven Bridges Platform API has two method to modify project members' permissions. This method uses the HTTP verb PUT, and the other uses the HTTP verb PATCH.
The difference between the two concerns the way that they update the information stored about the user. PATCH allows you to update just one part of the user's information --- for instance, just the value stored for the user's copy permission. On the other hand, a PUT request will fully overwrite the user's permission information. This means that when issuing a PUT request you must enter values for every key required to describe the user, even if the values for some keys are unchanged.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}/permissionshttps://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}/permissionshttps://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}/members/{username}/permissionsX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The short name of the project containing the project member.
project_owner
The owner of the project containing the project member.
username
The Seven Bridges Platform username of the user whose permissions you are overwriting.
fields
string
Selector specifying a subset of fields to include in the response.
Request body
In the body, you should enter a list of key-value pairs. The keys, and the values they take, are described in the following table.
"read"
Boolean: true or false
User can view file names, metadata, and workflows. They cannot view file contents.
All members of a project have read permissions by default. Even if you try setting read permissions to false, they will still default to true.
"write"
Boolean: true or false
User can add, modify, and remove files and workflows in a project.
Set value to true to assign the user write permission. Set to false to remove write permission.
"copy"
Boolean: true or false
User can view file content, copy, and download files from a project.
Set value to true to assign the user copy permission. Set to false to remove copy permission.
"execute"
Boolean: true or false
User can execute workflows and abort tasks in a project.
Set value to true to assign the user execute permission. Set to false to remove execute permission.
"admin"
Boolean: true or false
User can modify another user's permissions on a project, add or remove people from the project and manage funding sources. They also have all of the above permissions.
Set value to true to assign the user admin permission. Set to false to remove admin permission.
PUT /v2/projects/rfranklin/my-project/members/crick/permissions HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -X PUT --data-binary "@permissions-for-crick.json" -H "X-SBG-Auth-Token: ce7ae5ab85e946599298e88a3430fba0" 'http://api.sbgenomics.com/v2/projects/rfranklin/my-project/members/crick/permissions'{
"read": true,
"write": true,
"copy": true,
"execute": true,
"admin": false
}{
"write": true,
"read": true,
"copy": true,
"execute": true,
"admin": false
}List files (primary method)
This call returns a list of all files in a specified project with specified properties that you can access. For each file, the call returns:
- Its ID
- Its filename
The project to find files from is specified as a query parameter in the call. Don't forget that projects on the Platform are specified by their short names.
Further file properties to filter by can also be specified as query parameters.
File IDs
The file IDs returned by this call are useful for issuing further queries to get more information about a particular file.
https://api.sbgenomics.com/v2/fileshttps://eu-api.sbgenomics.com/v2/fileshttps://gcp-api.sbgenomics.com/v2/filesAlias call
There is a second method for listing files in a project: GET projects/{project_owner}/{project_name}/files. The call listed here is the primary and preferred method for performing this operation.
Since file filtering is a powerful feature, we have included some example usages.
Example 1: List all files in the project 'my-project':
Tips for filtering
When filtering on any resource, including the same field several times with different filtering criteria results in an implicit OR operation for that field and the different criteria.
When filtering by different specified fields, an implicit AND is performed between those criteria. Thus, the call in Example 3 above would return files matching the specified project AND sample ID AND library.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Query Parameters
You can use query parameters, listed in the table below, to return specific results. See the tip box below for details on OR and AND operations while filtering. Below the table, you'll see examples of API requests using various parameters.
project
required if "parent" is not used
string
Specified in the following format: {project_owner}/{project}. project_owner is the owner of the project you are listing files from, while project is the project's short name.
Should not be used together with parent. If parent is used, the call will list the content of the specified folder, within the project to which the folder belongs. If project is used, the call will list the content at the root of the project's files.
parent
required if "project" is not used
string
ID of the folder whose content you want to list.
Should not be used together with project. If parent is used, the call will list the content of the specified folder, within the project to which the folder belongs. If project is used, the call will list the content at the root of the project's files.
name
string
List file with this name. Note that the name must be an exact complete string for the results to match.
Multiple names can be separated by an OR operation, as shown in example 4 below. The OR operation is implied when the same parameter is queried multiple times in the same API request
metadata.{field}
string
List only files with that have the specified value in metadata field.
Multiple instances of the same metadata field are implicitly separated by an OR operation. Conversely, different metadata fields are implicitly separated by an AND operation, as shown in example 3 below.
origin.task
string
List only files produced by task specified by ID in this field
string
List files containing this tag. Note that the tag must be an exact complete string for the results to match. Multiple tags can be separated by an OR operation, as shown in example 5 below. The OR operation is implied when the same parameter is queried multiple times in the same API request.
Keep in mind that tags are different from metadata. Learn more about tagging your files on the Platform.
List files in the Public Reference Files repository
The Seven Bridges Public Reference Files repository is specified in the same way as a project on the Platform by an id of admin/sbg-public-data. You can pass this query parameter using project=admin/sbg-public-data.
Limit your results
Don't forget that you can use the pagination query parameter limit to restrict the number of files returned by this call.
Set the query parameter fields to _all to display tags within the response body, since tags is not automatically displayed in the response body.
GET /v2/files?project=rfranklin/my-project HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files?project=RFranklin/my-project"Example 2: List all files in 'my-project' with a specific sample ID
GET /v2/files?project=rfranklin/my-project&metadata.sample_id=SAMPLE1 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files?project=RFranklin/my-project&metadata.sample_id=SAMPLE1"Example 3: List all files in 'my-project' that were produced by a specific task with a specific library and sample ID:
GET /v2/files?rfranklin/project=my-project&metadata.sample_id=ERR315335&metadata.library_id=HiSeqX_R HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files?project=my-project&metadata.sample_id=ERR315335&origin.task=1262d968-1fda-4f06-a755-917a53a03e7e"Example 4: List all files in 'my-project' matching the exact names included in the query parameters:
GET /v2/files?project=rfranklin/my-project&name=dbsnp_137.b37.vcf&name=1000G_phase1.indels.b37.vcf&name=Mills_and_1000G_gold_standard.indels.b37.sites.vcf HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files?project=my-project&name=dbsnp_137.b37.vcf&name=1000G_phase1.indels.b37.vcf&name=Mills_and_1000G_gold_standard.indels.b37.sites.vcf"Example 5: List all files in 'my-project' matching the exact tags included in the parameters:
GET /v2/files?project=rfranklin/my-project&tag=test1b&tag=my_first_project&fields=_all HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files?project=franklin/my-project&tag=test1b&tag=my_first_project"{
"href": "https://api.sbgenomics.com/v2/files?offset=0&limit=25&project=RFranklin/my-project",
"items": [
{
"href": "https://api.sbgenomics.com/v2/files/568cf5dce4b0307bc0462060",
"id": "568cf5dce4b0307bc0462060",
"name": "1000G_phase1.indels.b37.vc",
"project": "RFranklin/my-project"
},
{
"href": "https://api.sbgenomics.com/v2/files/566aad1de4b0c560b469ea80",
"id": "566aad1de4b0c560b469ea80",
"name": "1000G_omni2.5.b37.vcf",
"project": "RFranklin/my-project"
},
{
"href": "https://api.sbgenomics.com/v2/files/568cf5f4e4b0307bc0462062",
"id": "568cf5f4e4b0307bc0462062",
"name": "1000G_phase1.snps.high_confidence.b37.vcf",
"project": "RFranklin/my-project"
}
],
"links": []
}List files (secondary method)
This call lists the files in the specified project. It is an alias for the call list files and redirects to that path.
Alias call
Note that since this is an alias for another call, the call cannot be made directly from all applications. In particular, to send the call using cURL, use the cURL option -L to redirect the path of this call to https://api.sbgenomics.com/v2/files?{project_owner}/{project}.
Alternatively, to list all files, you can simply use the call list files.
https://api.sbgenomics.com/v2/projects/{project_owner}/{project}/fileshttps://eu-api.sbgenomics.com/v2/projects/{project_owner}/{project}/fileshttps://gcp-api.sbgenomics.com/v2/projects/{project_owner}/{project}/filesReferring to your project
Note that project_owner is always case-sensitive, and that project is not the project's name but its ID, or short name. For more information about identifying objects in the API, see the section on identifying objects.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
project
The short name of the project you are querying.
project_owner
The owner of the project you are querying.
List files in the Public Reference Files repository
The Seven Bridges Public Reference Files repository is specified in the same way as a project on the Platform by an id of admin/sbg-public-data. You can pass this query parameter using project=admin/sbg-public-data.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/projects/rfranklin/my-project/files HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -L "https://api.sbgenomics.com/v2/files?RFranklin/my-project" -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/projects/RFranklin/my-project/files"{
"href": "https://api.sbgenomics.com/v2/files/?offset=0&limit=25&project=RFranklin/my-project",
"items": [
{
"href": "https://api.sbgenomics.com/v2/files/568cf5dce4b0307bc0462060",
"id": "568cf5dce4b0307bc0462060",
"name": "my_reference.vcf",
"project": "RFranklin/my-project"
},
{
"href": "https://api.sbgenomics.com/v2/files/566aad1de4b0c560b469ea80",
"id": "566aad1de4b0c560b469ea80",
"name": "_1_unsorted.bam",
"project": "RFranklin/my-project"
},
{
"href": "https://api.sbgenomics.com/v2/files/568cf5f4e4b0307bc0462062",
"id": "568cf5f4e4b0307bc0462062",
"name": "unsorted.bam",
"project": "RFranklin/my-project"
}
],
"links": []
}Delete a file
This call removes a file from the Seven Bridges Platform. Files are specified by their IDs, which you can obtain by making the API call to list files.
https://api.sbgenomics.com/v2/files/{file_id}https://eu-api.sbgenomics.com/v2/files/{file_id}https://gcp-api.sbgenomics.com/v2/files/{file_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID of the file you want to delete.
DELETE /v2/files/565357a1e4b09c884b29334a HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X DELETE "https://api.sbgenomics.com/v2/files/565357a1e4b09c884b29334a"Get file details
This call returns details about a specified file. The call returns the file's name, its tags, and all of its metadata.
Files are specified by their IDs, which you can obtain by making the API call to list files in a project .
Learn more about metadata fields and their values on the Seven Bridges Platform. You can also learn more about working with tags on the Platform.
https://api.sbgenomics.com/v2/files/{file_id}https://eu-api.sbgenomics.com/v2/files/{file_id}https://gcp-api.sbgenomics.com/v2/files/{file_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID of the file whose details you want to GET.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/files/562e449060b274321afb6091 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 565357a1e4b09c884b29334a
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files/565357a1e4b09c884b29334a"{
"href": "https://api.sbgenomics.com/v2/files/566aad1de4b0c560b469ea80",
"id": "566aad1de4b0c560b469ea80",
"name": "_1_1000G_phase1.snps.high_confidence.b37.vcf",
"size": 363,
"project": "RFranklin/my-project",
"created_on": "2015-12-11T11:01:49Z",
"modified_on": "2015-12-11T11:01:49Z",
"storage": {
"type": "VOLUME",
"volume": "rfranklin/my_volume_s3",
"location": "bemo/demo_omed"
},
"origin": {},
"metadata": {
"file_type": "vcf",
"file_extension": "VCF"
},
"tags": [
"my first files",
"test 1b",
"big sample"
]
}Interpreting the response body:
- The object
storagedenotes the type of storage for the file which can be eitherPLATFORMorVOLUMEdepending on where the file is stored. - The object
origindenotes the task that produced the file, if it was created by a task on the Seven Bridges Platform. - The dictionary object
metadatalists the metadata fields and values for the file. - The object
tagslists the tags for the file. Learn more about tagging your files on the Platform.
Update file details
This call updates the name, the full set metadata, and tags for a specified file.
Files are specified by their IDs, which you can obtain by making the API call to list files in a project .
If you want to update metadata for multiple files, the recommended way is to do it in bulk considering the API rate limit (learn more).
Metadata
Learn more about metadata fields and their permissible values on the Seven Bridges Platform.
https://api.sbgenomics.com/v2/files/{file_id}https://eu-api.sbgenomics.com/v2/files/{file_id}https://gcp-api.sbgenomics.com/v2/files/{file_id}File names and IDs
Note that the file name is not the same as its ID. The ID is a hexadecimal string, automatically assigned to a file in a project. The file's name is a human-readable string. For information about identifying objects in the API, see the section on identifying objects.
Custom metadata fields
As well as the standard set of metadata fields that can be seen through the visual interface, you are also able to add custom metadata for your files. Custom metadata fields are user-defined key-value pairs that allow you to provide additional metadata associated to files on the Platform. Custom metadata can be added via the command line uploader or via the API, but not through the visual interface.
Custom metadata fields will not be visible on the visual interface, but their values can be retrieved by getting file details via the API.
The following rules apply to custom metadata fields:
- Keys and values are case sensitive unless explicitly treated differently by a tool or a part of the Platform.
- Maximum number of key-value pairs per file is 1000, including null-value keys.
- Keys and values are UTF-8 encoded strings.
- Maximum length of a key is 100 bytes (UTF-8 encoding).
- Maximum length of a value is 300 bytes (UTF-8 encoding).
Tags
You can use this API request to add or edit previously existing tags for your file. You can tag your files on the Platform with keywords to make it easier to identify and organize files you’ve imported from public datasets or copied between projects. Learn more about tagging your files on the Platform.
In addition to editing tags on your files, you can do the following via the API:
- Add tags to a file
- View tags you've set on your files
- Filter files by tags, using list files and specifying the required
tag.
Header Fields
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID of the file whose details you want to update.
fields
string
Selector specifying a subset of fields to include in the response.
name
string
The new name of the file.
metadata
dictionary of key-value pairs. The keys and values are strings.
The metadata fields and their values that you want to update.
tags
array
The tags you want to update.
Notice that the metadata contains only the fields specified in the request body.
PATCH /v2/files/562e449060b274321afb6091 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 565357a1e4b09c884b29334a
curl --data '{"metadata": {disease_type: "Acute Myeloid Leukemia"}} -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X PATCH "https://api.sbgenomics.com/v2/files/565357a1e4b09c884b29334a"In the example below, I have submitted a request to change the file name to "1_1000Genomes_phase1.snps.high_confidence.b37.vcf" and to have the metadata contain only the field disease_type with value "Acute Myeloid Leukemia". This request also adds the tags test 1b and sample.
{
"name": "1_1000Genomes_phase1.snps.high_confidence.b37.vcf",
"metadata": {
"disease_type": "Acute Myeloid Leukemia"
},
"tags": ["test 1b", "sample"]
}{
"href": "https://api.sbgenomics.com/v2/files/566aad1de4b0c560b469ea80",
"id": "566aad1de4b0c560b469ea80",
"name": "1_1000Genomes_phase1.snps.high_confidence.b37.vcf",
"size": 363,
"project": "RFranklin/my-project",
"created_on": "2015-12-11T11:01:49Z",
"modified_on": "2016-01-07T12:22:12Z",
"origin": {},
"metadata": {
"disease_type": "Acute Myeloid Leukemia",
},
"tags":[
"test 1b",
"sample"
]
}Interpreting the response body:
- The object
origindenotes the task that produced the file, if it was created by a task on the Seven Bridges Platform. - The dictionary object
metadatalists the metadata fields and values for the file. - The object
tagslists the tags for the file. Learn more about tagging your files on the Platform.
Copy a file between projects
This call copies the specified file to a new project. Files retain their metadata when copied, but may be assigned new names in their target project.
To make this call, you should have copy permission within the project you are copying from.
If you want to copy multiple files, the recommended way is to do it in bulk considering the API rate limit (learn more).
https://api.sbgenomics.com/v2/files/{file_id}/actions/copyhttps://eu-api.sbgenomics.com/v2/files/{file_id}/actions/copyhttps://gcp-api.sbgenomics.com/v2/files/{file_id}/actions/copyfile_ids
Recall from the API Overview that the file_id is a hexadecimal string.
You can get the file_id for a file by making the call to list files within a specified project (primary method).
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID for the file you are querying. It can be obtained by making the call to list your files (primary method).
fields
string
Selector specifying a subset of fields to include in the response.
"project"
required
string
The name of the project you want to copy the file to
"name"
string
The new name the file will have in the target project.
If its name will not change, omit this key.
{
"project": "RFranklin/my-project",
"name": "new-file"
}The response gives the full specification of the file, and its metadata.
POST v2/files/568e69ade4b0307bc0464164/actions/copy HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl --data '{"project": "RFranklin/my-project", "name": "new-file"}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/files/568e69ade4b0307bc0464164/actions/copy" {
"href": "https://api.sbgenomics.com/v2/files/569637cce4b0b65fcb306ae5",
"id": "569637cce4b0b65fcb306ae5",
"name": "new-file",
"size": 68425,
"project": "RFranklin/my-project",
"created_on": "2016-01-13T11:41:00Z",
"modified_on": "2016-01-13T11:41:00Z",
"origin": {},
"metadata": {
"sample_id": "E16201_pool35_L1756",
"library_id": "hg19",
"platform_unit_id": "C18_99",
"platform": "IonTorrent",
"quality_scale": "sanger"
}
}Copy multiple files between projects
This call allows you to copy files between projects. Unlike the call to copy a file between projects, this call lets you batch the copy operation and copy a list of files at a time.
File IDs
Note that a file's ID is dependent on the project it is contained in. So, when you copy files from one project to another, their IDs will be different in the target project.
The file names, however, do not change by copying, except where copying would yield non-unique file names in a project. For details of this use case, see the tipbox at the bottom of the page.
https://api.sbgenomics.com/v2/action/files/copyhttps://eu-api.sbgenomics.com/v2/action/files/copyhttps://gcp-api.sbgenomics.com/v2/action/files/copyFiles are specified by their IDs, which you can obtain by making the API call to list all files accessible to you.
Request body
In the body, you should enter a list of key-value pairs. The keys, and the values they take, are described in the following table.
project
string
The name of the project you want to copy into.
file_ids
a list of strings
The IDs of the files you want to copy.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
POST /v2/action/files/copy HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96curl --data '{"project": "RFranklin/my-project", "file_ids": ["5655df71e4b08c5d86970945", "5721e1bee4b0d8becbf4ebf0"]}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/action/files/copy"{
"project": "RFranklin/my-project",
"file_ids": ["5655df71e4b08c5d86970945", "5721e1bee4b0d8becbf4ebf0"]
}{
"5655df71e4b08c5d86970945": {
"status": "OK",
"new_file_id": "568cf5f4e4b0307bc0462062",
"new_file_name": "sorted.bam"
}
}Interpreting the request body
The request returns an object "new_file_name" for every file copied.
The "new_file_name" will be the same as the file's old name in all cases except for the case in which you already have a file with that name in the target project. If an identically-named file exists in the project, then the copied file will be automatically renamed by prefixing it with an increment of 1. For instance, if I copy the file named file.ext to my project, and there already exists a file.ext there, then my incoming file will be renamed 1_file.ext.
It is not possible to re-name files other than by this automatic procedure with this call. If you want to copy and rename a file, use the alternative (non-batch) call to copy a file. This restriction optimizes the batch request: it adds 100ms per file to rename it during copying, so if copying 100 files, it would take 10s longer to rename all of them.
Get downloadable URL for a file
This call returns a URL that you can use to download the specified file.
https://api.sbgenomics.com/v2/files/{file_id}/download_infohttps://eu-api.sbgenomics.com/v2/files/{file_id}/download_infohttps://gcp-api.sbgenomics.com/v2/files/{file_id}/download_infoX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
fie_id
The ID of the file whose download URL you want to get.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/files/56534e57e4b093830b6e967b/download_info HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files/56534e57e4b093830b6e967b/download_info"{
"url": "https://main.s3.amazonaws.com/050177a9-ecff-430c-96f8-54561a0c301e%2Btest-text.txt?response-content-disposition=attachment%3Bfilename%3Dtest-text.txt&response-content-type=application%2Foctet-stream&AWSAccessKeyId=AKIAIZUEXM5REGIZ56VA&Expires=1452345802&Signature=4v3DEiBMyiyLw%2F3VGyJUlwSyw28%3D"
}Get a file's metadata
This call returns the metadata values for the specified file.
Metadata on the Platform
Learn more about metadata fields and their values on the Seven Bridges Platform.
Files are specified by their IDs, which you can obtain by making the API call to list files in a project .
https://api.sbgenomics.com/v2/files/{file_id}/metadatahttps://eu-
api.sbgenomics.com/v2/files/{file_id}/metadatahttps://gcp-api.sbgenomics.com/v2/files/{file_id}/metadataX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID of the file whose details you want to GET.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/files/562e449060b274321afb6091/metadata HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 565357a1e4b09c884b29334a
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/files/565357a1e4b09c884b29334a/metadata"{
"sample_id": "E16201_pool35_L1756",
"library_id": "hg19",
"platform_unit_id": "C18_99",
"platform": "IonTorrent",
"quality_scale": "sanger"
}Modify a file's metadata
This call modifies the metadata values for the specified file.
Metadata on the Platform
Learn more about metadata fields and their values on the Seven Bridges Platform.
Files are specified by their IDs, which you can obtain by making the API call to list files in a project .
https://api.sbgenomics.com/v2/files/{file_id}/metadatahttps://eu-api.sbgenomics.com/v2/files/{file_id}/metadatahttps://gcp-api.sbgenomics.com/v2/files/{file_id}/metadataPUT and PATCH
The API has two method to modify file metadata. This method uses the HTTP verb PATCH, and the other uses the HTTP verb PUT.
- The difference between the two concerns the way that they update the information stored about the file.
PATCHallows you to update just one metadata field. On the other hand, aPUTrequest will fully overwrite the values for all metadata fields. This means that when issuing aPUTrequest you must enter values for every key required to specify the metadata, even if the values for some keys are unchanged. If you don't specify a value for a given metadata field when making thePUTrequest, then any existing value for that field will be reset.
Custom metadata fields
Apart from the standard set of metadata fields that can be seen through the visual interface, you are also able to add custom metadata for your files. Custom metadata fields are user-defined key-value pairs that allow you to provide additional metadata associated to files on the Platform. Custom metadata can be added via the command line uploader or via the API, but not through the visual interface.
The following rules apply to custom metadata fields:
- Keys and values are case sensitive unless explicitly treated differently by a tool or a part of the Platform.
- Maximum number of key-value pairs per file is 1000.
- Keys and values are UTF-8 encoded strings.
- Maximum length of a key is 100 bytes (UTF-8 encoding).
- Maximum length of a value is 300 bytes (UTF-8 encoding).
- Null values and keys are ignored and not counted towards the 1000 key-value pair limit.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID of the file whose metadata you want to update.
fields
string
Selector specifying a subset of fields to include in the response.
Freeform -- enter any key.
string
The value for the corresponding key
{
"sample origin": "712345"
}PATCH /v2/files/562e449060b274321afb6091/metadata HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 565357a1e4b09c884b29334a
curl --data '{"foo": "bar"}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X PATCH "https://api.sbgenomics.com/v2/files/5657152ee4b0298dd2cdf724/metadata"The response contains the full metadata specification for the file, including the values that you just added with the request.
{
"library_id": "12345",
"platform": "my_platform",
"sample origin": "712345"
"foo": "bar",
"my_key_1": "my_value_1",
"my_key_2": "my_value_2"
}Overwrite a file's metadata
This call changes the metadata values for the specified file.
Metadata on the Platform
Learn more about metadata fields and their values on the Seven Bridges Platform.
Files are specified by their IDs, which you can obtain by making the API call to list files in a project .
https://api.sbgenomics.com/v2/files/{file_id}/metadatahttps://eu-api.sbgenomics.com/v2/files/{file_id}/metadatahttps://gcp-api.sbgenomics.com/v2/files/{file_id}/metadataPUT and PATCH
The Seven Bridges Platform API has two method to modify file metadata. This method uses the HTTP verb PUT, and the other uses the HTTP verb PATCH.
The difference between the two concerns the way that they update the information stored about the user. PATCH allows you to update just one metadata field. On the other hand, a PUT request will fully overwrite the values for all metadata fields. This means that when issuing a PUT request you must enter values for every key required to specify the metadata, even if the values for some keys are unchanged. If you don't specify a value for a given metadata field when making the PUT request, then any existing value for that field will be reset.
Custom metadata fields
Apart from the standard set of metadata fields that can be seen through the visual interface, you are also able to add custom metadata for your files. Custom metadata fields are user-defined key-value pairs that allow you to provide additional metadata associated to files on the Platform. Custom metadata can be added via the command line uploader or via the API, but not through the visual interface.
The following rules apply to custom metadata fields:
- Keys and values are case sensitive unless explicitly treated differently by a tool or a part of the Platform.
- Maximum number of key-value pairs per file is 1000.
- Keys and values are UTF-8 encoded strings.
- Maximum length of a key is 100 bytes (UTF-8 encoding).
- Maximum length of a value is 300 bytes (UTF-8 encoding).
- Null values and keys are ignored and not counted towards the 1000 key-value pair limit.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
file_id
The ID of the file whose details you want to overwrite.
fields
string
Selector specifying a subset of fields to include in the response.
Request body
In the body of the request, you should enter key-value pairs corresponding to metadata fields and their values.
Freeform -- enter any string
string
The value for the corresponding key
Since you need to specify values for all metadata fields, it can be easier to send the data as a file, using the option --data-binary in cURL.
PUT /v2/files/5655df71e4b08c5d86970945/metadata HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 565357a1e4b09c884b29334a
curl --data-binary "@metadata.json" -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X PUT "https://api.sbgenomics.com/v2/files/5655df71e4b08c5d86970945/metadata"{
"foo": "bar",
"my_key_1": "my_value_1",
"my_key_2": "my_value_2",
"platform": "my_platform",
"library_id": "12345"
}{
"library_id": "12345",
"platform": "my_platform",
"foo": "bar",
"my_key_1": "my_value_1",
"my_key_2": "my_value_2"
}Create a folder
/files
This call creates a new folder.
Every project on the Seven Bridges Platform is represented by a root folder which contains all the files associated with a particular project. You can create nesting folders and subfolders within this root folder by using this API request.
Once you've created a folder, you can move or copy (coming soon) files between folders to populate your newly created folder.
To list the contents of the main project folder, first make the API request to get project details which will return the ID of the main folder (key: root_folder). Next, use the list folder contents call and specify this ID.
https://api.sbgenomics.com/v2/fileshttps://eu-api.sbgenomics.com/v2/fileshttps://gcp-api.sbgenomics.com/v2/files X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
name
required
String
The name of the folder. It shouldn't begin with "__".
type
required
Enum
folder
parent
String
Specifies the ID of the parent folder for the new folder.
You should either specify a parent folder or the project name (see list folder contents for instructions on how to find the folder ID).
project
String
Project ID (username/project_name).
You should either specify a project name or the parent folder ID.
POST /v2/files HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
Content-Type: application/json
curl -X POST -H "X-SBG-Auth-Token: c2e05946fb9a494ab5c19c72a94cb4ac" -H "Content-Type: application/json" -d '{
"name" : "my_new_folder",
"type" : "folder",
"parent": "57fb98c51c94d72f08ba0544"
}{
"name": "my_new_folder",
"parent": "57fba0611c94d72f08ba0550",
"type": "FOLDER"
}{
"href": "https://api.sbgenomics.com/v2/files/57fba0611c94d72f08ba0550",
"id": "5800b406e4b07ecb1445de83",
"name": "my_new_folder",
"parent": "57fba0611c94d72f08ba0550",
"type": "FOLDER",
"created_on": "2016-10-10T14:06:25Z",
"modified_on": "2016-10-10T14:06:25Z"
}List folder contents
files/{folder_id}/list
This call lists the contents of the specified folder.
https://api.sbgenomics.com/v2/files/{folder_id}/listhttps://eu-api.sbgenomics.com/v2/files/{folder_id}/listhttps://gcp-api.sbgenomics.com/v2/files/{folder_id}/listX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
limit
integer
The maximum number of collection items to return for a single request. Minimum value is 1. The maximum value is 100 and the default value is 50. This is a pagination-specific attribute.
offset
integer
The zero-based starting index in the entire collection of the first item to return. The default value is 0. This is a pagination-specific attribute.
GET /v2/files/6282d5e2121d43e7900e9d52b15845e7/list HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
Content-Type: application/jsoncurl -X GET -H "X-SBG-Auth-Token: c2e05946fb9a494ab5c19c72a94cb4ac" -H "Content-Type: application/json" "http://api.sbgenomics.com/v2/files/57fb98c51c94d72f08ba0544/list"{
"href": "https://api.sbgenomics.com/v2/files/57fb98c51c94d72f08ba0544/list?offset=0&limit=5",
"items": [
{
"href": "https://api.sbgenomics.com/v2/files/57fba0581c94d72f08ba054e",
"id": "57fba0581c94d72f08ba054e",
"name": "folder-name-1",
"project": "rfranklin/my-project",
"parent": "57fb98c51c94d72f08ba0544",
"type": "FOLDER"
},
{
"href": "https://api.sbgenomics.com/v2/files/57fba04c1c94d72f08ba054a",
"id": "57fba04c1c94d72f08ba054a",
"name": "file-name-1",
"project": "rfranklin/my-project",
"parent": "57fb98c51c94d72f08ba0544",
"type": "FILE"
},Copy a file between folders
This call copies the specified file to another folder within the same project. Files retain their metadata when copied, but may be assigned new names in their target project.
https://api.sbgenomics.com/v2/files/{file_id}/actions/copyhttps://eu-api.sbgenomics.com/v2/files/{file_id}/actions/copyhttps://gcp-api.sbgenomics.com/v2/files/{file_id}/actions/copyX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
parent
required
String
Specifies the target folder by using its ID.
To find out the folder ID, use the list folder contents call for its parent folder.
name
String
Specifies a new name for a file in case you want to rename it.
If you want to use the same name, omit this key.
{
"parent": "57ff702e1c94d72f08ba34e8",
"name": "1000G_omni2.5.hg38.vcf"
}POST /v2/files/{file_id}/actions/copy HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
Content-Type: application/jsoncurl --data '{"project": "RFranklin/my-project", "name": "new-file", "parent: "57fb98c51c94d72f08ba0544"}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/files/568e69ade4b0307bc0464164/actions/copy"
{
"href": "https://api.sbgenomics.com/v2/files/57fba0611c94d72f08ba0550",
"id": "57ff71c71c94d72f08ba34ed",
"name": "1000G_omni2.5.hg38.vcf",
"size": 208485995,
"project": "rfranklin/my-project-3",
"parent": "57ff702e1c94d72f08ba34e8",
"type": "FILE",
"created_on": "2016-10-13T11:36:39Z",
"modified_on": "2016-10-13T11:36:39Z",
"storage": {
"type": "PLATFORM"
},
"origin": {},
"tags": [
"WGS",
"hg38"
],
"metadata": {}
}Move a file between folders
This call moves a file from one folder to another. Moving of files is only allowed within the same project.
https://api.sbgenomics.com/v2/files/{file_id}/actions/movehttps://eu-api.sbgenomics.com/v2/files/{file_id}/actions/movehttps://gcp-api.sbgenomics.com/v2/files/{file_id}/actions/moveX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
parent
required
String
Specifies the target folder by using its ID.
To find out the folder ID, use the list folder contents call for its parent folder.
name
String
Specifies a new name for a file in case you want to rename it.
If you want to use the same name, omit this key.
POST /v2/files/{file_id}/actions/move HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
Content-Type: application/jsoncurl --data '@move.json' -X POST -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "Content-Type: application/json" 'https://api.sbgenomics.com/files'{
"parent": "57ff702e1c94d72f08ba34e8",
"name": "1000G_omni2.5.hg38.vcf"
}Delete a folder
This call deletes a folder. Only an empty folder can be deleted.
https://api.sbgenomics.com/v2/files/{folder_id}https://eu-api.sbgenomics.com/v2/files/{folder_id}https://gcp-api.sbgenomics.com/v2/files/{folder_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
DELETE /v2/files/{folder_id} HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
Content-Type: application/jsoncurl -X DELETE -H "X-SBG-Auth-Token: c2e05946fb9a494ab5c19c72a94cb4ac" -H "Content-Type: application/json" "http://api.sbgenomics.com/v2/files/5800cd381c94d72f08ba375b"List current multipart uploads
This call returns the list of ongoing uploads.
https://api.sbgenomics.com/v2/upload/multiparthttps://eu-api.sbgenomics.com/v2/upload/multiparthttps://gcp-api.sbgenomics.com/v2/upload/multipartX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
GET /v2/upload/multipart HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/upload/multipart"{
"items": [
{
"href": "http://api.sbgenomics.com/v2/upload/multipart/ezBaGmsWvyLwLjDdw3WNXXfs0EK4GpcHXijP37fP7o1jbdh24IAFEF7New5wYyli",
"project": "RFranklin/my-project",
"name": "1000G_phase1.indels.b37.vc",
"initiated": "2016-03-11T15:15:21Z",
"upload_id": "ezBaGmsWvyLwLjDdw3WNXXfs0EK4GpcHXijP37fP7o1jbdh24IAFEF7New5wYyli"
},
{
"href": "http://api.sbgenomics.com/v2/upload/multipart/X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm",
"project": "RFranklin/my-project",
"name": "1000G_omni2.5.b37.vcf",
"initiated": "2016-03-11T16:05:28Z",
"upload_id": "X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm"
}
]
}Get details of a multipart upload
This call will return the details of an active multipart upload.
The upload is referenced by its ID as returned by a call to initialize a multipart upload or list current multipart uploads.
https://api.sbgenomics.com/v2/upload/multipart/{upload_id}https://eu-api.sbgenomics.com/v2/upload/multipart/{upload_id}https://gcp-api.sbgenomics.com/v2/upload/multipart/{upload_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
upload_id
The ID of the upload. It can be obtained by initializing a new upload or by listing the ongoing multipart uploads.
list_parts
Boolean: true or false
If true, also return a list of parts that have been reported as completed for this multipart upload.
GET /v2/upload/multipart/ezBaGmsWvyLwLjDdw3WNXXfs0EK4GpcHXijP37fP7o1jbdh24IAFEF7New5wYyli HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/upload/multipart"{
"upload_id": "X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm",
"project": "RFranklin/my-project",
"name": "1000G_omni2.5.b37.vcf",
"initiated": "2016-01-01T00:00:00Z",
"parallel_uploads": true,
"part_size": 1073741824,
"uploaded_parts_count": 1,
"parts": [
{
"part_number": 1,
"response": {
"headers": {
"ETag": "43a5e128440f2b6602badfdabe610f30"
}
}
}
]
}Initialize a multipart upload
This call initializes a multipart file upload.
https://api.sbgenomics.com/v2/upload/multiparthttps://eu-api.sbgenomics.com/v2/upload/multiparthttps://gcp-api.sbgenomics.com/v2/upload/multipartX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
overwrite
Boolean: true or false
If overwrite is set to true and a file already exists under the name specified in the request, the existing file will be deleted and a new one created in its place.
Request body
In the body, you should enter a list of key-value pairs. The keys, and the values they take, are described in the following table.
project
Required
String
The name of the project you want to upload a file to.
parent
String
The ID of the folder to which the item is being uploaded.
Should not be used together with project. If parent is used, the upload will take place into the specified folder, within the project to which the folder belongs. If project is used, the items will be imported to the root of the project's files.
name
Required
String
The name of the file you are about to upload. This must be unique in the project, unless you are also enabling the overwrite query parameter.
Allowed characters in file names are all alphanumerics and special characters except slash (/). File names can’t be longer than 255 characters.
size
Integer
The size of the file that will be uploaded. This can be used to track progress of an ongoing upload, but is otherwise optional.
part_size
Integer
The preferred size for upload parts. If omitted or set to a value that is incompatible with the cloud storage provider, a default value will be used.
md5
String
32-byte hexadecimal MD5 checksum of the file. This value is currently only stored but is not used by the Platform.
POST /v2/upload/multipart HTTP/1.1
Host: api.sbgenomics.com
Content-Type: application/json
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
{
"project": "RFranklin/my-project",
"name": "CanFam3.1.dna_rm.toplevel.fa.gz",
"part_size": 5242880,
"size": 433759572
}curl --data '{"project": "RFranklin/my-project", "name": "CanFam3.1.dna_rm.toplevel.fa.gz", "part_size": 5242880, "size": 433759572}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/upload/multipart"{
"project": "RFranklin/my-project",
"name": "CanFam3.1.dna_rm.toplevel.fa.gz",
"size": 433759572,
"upload_id": "oSZ5rOjMQa34UykB4FiPdhkCalLVrcQjxjKPkAT69skWgOPlOvcvGaqEJ7SI1o4w",
"part_size": 5242880,
"parallel_uploads": true
}Get upload URL for a file part
This call returns the signed URL required to upload a part of a multipart upload. Once you have obtained this URL for your file part, you can make a PUT request to it with the file part as the request body.
https://api.sbgenomics.com/v2/upload/multipart/{upload_id}/part/{part_number}https://eu-api.sbgenomics.com/v2/upload/multipart/{upload_id}/part/{part_number}https://gcp-api.sbgenomics.com/v2/upload/multipart/{upload_id}/part/{part_number}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
upload_id
The ID for the upload, returned by the call to initialize a multipart upload.
part_number
The number of the file part you are uploading. Part numbers start from 1.
Response body
The response object contains information about the URL to which you should upload the file part. The information is structured using the following key-value pairs:
method
String
The HTTP method to use when making the HTTP part upload request.
url
String
The URL to which to make the HTTP part upload request.
expires
Integer
ISO 8601 combined date and time representation in Coordinated Universal Time (UTC) by when the HTTP part upload request should be made.
headers
Object
A map of headers and values that should be set when making the HTTP part upload request.
report
Object
See the structure of the report object section below for an explanation of the report object.
success_codes
Array of Integers
A list of status codes returned by the HTTP part upload request that should be recognized as success.
A successful part upload request should be reported back to the API in a call to report an uploaded file part by passing the information collected from the report object.
Structure of the report object
This object instructs you which pieces of information need to be collected from a successful response to the HTTP part upload request.
headers
Array of Strings
A list of HTTP headers whose values should be collected from a successful response to the HTTP part upload request.
body
Object
Reserved for future use
GET /v2/upload/multipart/ezBaGmsWvyLwLjDdw3WNXXfs0EK4GpcHXijP37fP7o1jbdh24IAFEF7New5wYyli/part/1 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/upload/multipart/EXAMPLE_ID/part/1"{
"method": "PUT",
"url": "https://sbg-vs2-devel.s3.amazonaws.com/aa8a1030-7e27-4da4-b42b-39658b795d61%2BCanFam3.1.dna_rm.toplevel.fa.gz?uploadId=lMllZ7WIWqHsCNj9IKV4VytwZOy0.4ZKFPDD73Cw6I745a3xFXKZLHrqDi0kZt0jTm25PYJqNfEJDF9OaJ6Xvg8vLv9K7SJ.RLiCczfy6ieGCJzNQd78vmSK3a9Bkgx2&partNumber=1&AWSAccessKeyId=AKIAJF4ANIHWSCZA724Q&Expires=1459113561&Signature=3myy2S6960C11jkmjX24WApZwNo%3D",
"expires": "2016-02-27T15:55:38Z",
"headers": {},
"report": {
"success_codes": [
200
],
"headers": [
"ETag"
]
}
}Report an uploaded part
This call allows you to report the upload of a file part.
https://api.sbgenomics.com/v2/upload/multipart/{upload_id}/parthttps://eu-api.sbgenomics.com/v2/upload/multipart/{upload_id}/parthttps://gcp-api.sbgenomics.com/v2/upload/multipart/{upload_id}/partX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
upload_id
The ID for the upload, returned by the call to initialize a multipart upload.
Request body
In the body of the request, you should enter a JSON object key-value pairs describing the report. The keys, and their permitted values, are described below.
part_number
Integer
The number of the file part you are reporting. Part numbers start from 1.
response
Object
This object should contain the information collected from a successful HTTP part upload request.
See the formatting the response object section below for an explanation of its structure.
Formatting the response object
When reporting a part, the structure of the response object is different from that of the report object received when getting a part upload URL. Assuming that you have collected the information from the HTTP part upload request, you should format the response object in this call as a set of key-value mappings. The keys in these mappings are the headers and other response elements described in getting upload URL for a file part, and their values are the strings that you have collected from the HTTP part upload request.
See the example below for an illustration of how to format a part report request when the Seven Bridges Platform stores your files on Amazon S3.
headers
Object of String keys to String values
A map of header keys from the Get upload URL for a file part to their values returned by the successful HTTP part upload request you've made.
body
Object
Reserved for future use
{
"part_number": 1,
"response": {
"headers": {
"ETag": "be96ac61fa156d2d71ae61608f992554"
}
}
}POST /v2/upload/multipart/ezBaGmsWvyLwLjDdw3WNXXfs0EK4GpcHXijP37fP7o1jbdh24IAFEF7New5wYyli/part HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl --data '{"part_number": 1, "response": {"headers": {"ETag": "be96ac61fa156d2d71ae61608f992554"}}}' -s -H "X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/upload/multipart/ezBaGmsWvyLwLjDdw3WNXXfs0EK4GpcHXijP37fP7o1jbdh24IAFEF7New5wYyli/part"Report uploaded parts
This call allows you to report the upload multiple file parts at once.
https://api.sbgenomics.com/v2/upload/multipart/{upload_id}https://eu-api.sbgenomics.com/v2/upload/multipart/{upload_id}https://gcp-api.sbgenomics.com/v2/upload/multipart/{upload_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application_json
upload_id
The ID for the upload, returned by the call to initialize a multipart upload.
Request body
In the body of the request, you should enter key-value pairs describing the task. The keys, and their permitted values, are described below.
parts
Array of Objects
This key should contain an array of objects describing the individual part upload reports. Each of these objects should be formatted exactly as the whole body of the report an uploaded part call.
POST /v2/upload/multipart/EXAMPLE_ID HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
{
"parts": [
{
"part_number": 1,
"response": {
"headers": {
"ETag": "9f1b6da2989615a414e8b00a27d20b0c"
}
}
}
]
}curl --data '@report_parts.json' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/upload/multipart/EXAMPLE_ID"{
"parts": [
{
"part_number": 1,
"response": {
"headers": {
"ETag": "9f1b6da2989615a414e8b00a27d20b0c"
}
}
},
{
"part_number": 2,
"response": {
"headers": {
"ETag": "266f8e5c06b6cc1495646fc48b3f2f0e"
}
}
}
]
}Complete a multipart upload
This call must be issued to report the completion of a file upload.
An optional list of remaining parts may be given in the body of this request. The format of this list is the same as described in report uploaded parts.
https://api.sbgenomics.com/v2/upload/multipart/{upload_id}/completehttps://eu-api.sbgenomics.com/v2/upload/multipart/{upload_id}/completehttps://gcp-api.sbgenomics.com/v2/upload/multipart/{upload_id}/completeX-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
upload_id
The ID for the upload, returned by the call to initialize a multipart upload.
POST /v2/upload/multipart/X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm/complete HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X DELETE "https://api.sbgenomics.com/v2/upload/multipart/X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm/complete"{
"href": "http://api.sbgenomics.com/v2/files/36faaf29f5b4568b3c86e09d",
"path": "/Projects/e27c4f6b-5e41-4ff2-74a3-e34a70af9ace/CanFam3.1.dna_rm.toplevel.fa.gz",
"id": "36faaf29f5b4568b3c86e09d",
"project": "RFranklin/my-project",
"name": "CanFam3.1.dna_rm.toplevel.fa.gz",
"type": "file",
"size": 433759572,
"created_on": "2016-02-27T16:36:41Z",
"modified_on": "2016-02-27T16:36:41Z"
}Abort a multipart upload
This call aborts an ongoing upload.
https://api.sbgenomics.com/v2/upload/multipart/{upload_id}https://eu-api.sbgenomics.com/v2/upload/multipart/{upload_id}https://gcp-api.sbgenomics.com/v2/upload/multipart/{upload_id}X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
required
application/json
upload_id
The ID for the upload, returned by a call to initialize a multipart upload or to list current multipart uploads.
DELETE /v2/upload/multipart/X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74curl -s -H "X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74" -H "content-type: application/json" -X DELETE "https://api.sbgenomics.com/v2/upload/multipart/X5FXjV7JVCdg0cidZKIOOZRvAgahy9znuHq1PMsOZ85de6x53UOcJAcCDXANVTpm"Apps
These API calls below allow you to manage apps on the Seven Bridges Platform. Supported operations include listing apps in a given project, and in public apps. You can also copy apps between projects.
List all apps available to you
Get details of an app
Copy an app
Get raw CWL for an app
Add an app using raw CWL
Get raw CWL for an app revision
Get details of an app revision
List all apps available to you
This call lists all the apps available to you.
https://api.sbgenomics.com/v2/appshttps://eu-api.sbgenomics.com/v2/appshttps://gcp-api.sbgenomics.com/v2/appsPublic/private apps
Note that you can see all of the publicly available apps on the Seven Bridges Platform by setting the query parameter visibility to public. If you omit this parameter, you will see all your private apps, i.e. those in projects that you can access. Learn more about public apps in our documentation.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
fields
string
Selector specifying a subset of fields to include in the response.
project
string
Enter a project, in the form {project_owner}/{project_short_name} to restrict the results to apps from that project only.
visibility
string
Set this to public to see all public apps on the Seven Bridges Platform.
q
string
Enter one or more search terms to query apps using the q parameter. Learn more about querying below.
id
string
Use this parameter to query apps based on their ID.
Query apps
Use one or more search terms via the q parameter to query all apps that are available to you. An "and" operator is implied when using multiple search terms separated by a space. Further refine your query by specifying either the project containing the app or the project's owner.
Search terms should relate to the following app details:
- name
- label
- toolkit
- toolkit version
- category
- tagline
- description
For the query to return results, each term must match at least one of the fields that describe an app. For example, the first term can match the app's name while the second can match the app description. However, if any part of the search fails to match app details, the query is returned as null.
Example requests for querying apps
Query apps by any of the search terms
Use search terms to query apps by including them after the app parameter, as shown below.
GET /v2/apps?q=WGS SBG RNAQuery apps in a specific project
Use search terms to query apps in a specific project by entering the terms and then specifying the project name, as shown below.
GET /v2/apps?q=WGS SBG&project=username/project-nameQuery apps for a specific project owner
Use search terms to query apps belonging to a specific project owner by entering the terms and then specifying the name of the project owner, as shown below.
GET /v2/apps?q=WGS SBG&project_owner=usernameGET /v2/apps HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/apps" {
"href": "https://api.sbgenomics.com/v2/apps/",
"items": [
{
"href": "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/workflow",
"id": "RFranklin/my-project/workflow",
"name": "workflow"
},
{
"href": "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/fusion-transcript-detection-chimerascan",
"id": "RFranklin/my-project/fusion-transcript-detection-chimerascan",
"name": "fusion-transcript-detection-chimerascan"
},
{
"href": "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/somaticsniper-filters",
"id": "RFranklin/my-project/somaticsniper-filters",
"name": "somaticsniper-filters"
},
{
"href": "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/command-line-tool",
"id": "RFranklin/my-project/command-line-tool",
"name": "command-line-tool"
},
{
"href": "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/delly2-workflow",
"id": "RFranklin/my-project/delly2-workflow",
"name": "delly2-workflow"
},
]
}Get details of an app
This call returns information about the specified app. The app should be one in a project that you can access; this could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project.
https://api.sbgenomics.com/v2/apps/{app_id}https://eu-api.sbgenomics.com/v2/apps/{app_id}https://gcp-api.sbgenomics.com/v2/apps/{app_id}app_ids
Recall from the apps section in the API overview that the app_id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.
If the revision_number field is omitted, the latest revision of the app is returned
You can get the app_id for an app by making the call to list all apps available to you
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
app_id
The ID for the app you are querying. It can be obtained by making the call to list all apps available to you
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0"{
"href": "https://cgc-api.sbgenomics.com/v2/apps/rfranklin/my-project/cummerbundqc/0",
"id": "rfranklin/my-project/cummerbundqc/0",
"project": "rfranklin/my-project",
"name": "CummeRbundQC",
"revision": 0,
"raw": {
"sbg:toolAuthor": "Cole Trapnell/University of Washington",
"sbg:project": "rfranklin/my-project",
"requirements": [],
"id": "https://cgc-api.sbgenomics.com/rfranklin/my-project/cummerbundqc/0/raw/",
"sbg:toolkit": "CummeRbund",
"sbg:revision": 0,
"sbg:toolkitVersion": "2.8.2",
"stdout": "",
"outputs": [
{
"outputBinding": {
"glob": "*.zip",
"sbg:metadata": {},
"sbg:inheritMetadataFrom": "#cuffdiff_zip"
},
"type": [
"null",
"File"
],
"sbg:fileTypes": "ZIP",
"description": "Downloadable zipped report.",
"id": "#archive",
"label": "Report archive"
},
{
"outputBinding": {
"glob": "*.b64html",
"sbg:metadata": {},
"sbg:inheritMetadataFrom": "#cuffdiff_zip"
},
"type": [
"null",
"File"
],
"sbg:fileTypes": "B64HTML",
"description": "Base64 encoded HTML report prepared for easy viewing.",
"id": "#html",
"label": "Report"
}
],
"inputs": [
{
"sbg:category": "Input files",
"type": [
"File"
],
"sbg:fileTypes": "ZIP",
"id": "#cuffdiff_zip",
"description": "Zipped list of output tracking, tab delimited and INFO files.",
"inputBinding": {
"prefix": "--cuffzip",
"separate": true,
"sbg:cmdInclude": true
},
"label": "Archive of Cuffdiff output files"
},
{
"sbg:category": "Basic Options",
"type": [
"null",
"float"
],
"id": "#dispersion_threshold",
"description": "Changing this parameter sets threshold for the genes that are displayed on dispersion plot, namely it removes from the plot all genes that have dispersion lower than this value.",
"sbg:toolDefaultValue": "0.01",
"inputBinding": {
"prefix": "--dispthreshold",
"separate": true,
"sbg:cmdInclude": true
},
"label": "Dispersion plot threshold"
},
{
"sbg:category": "Basic Options",
"type": [
"null",
"float"
],
"id": "#density_threshold",
"description": "Changing this parameter sets threshold for the genes that are displayed on both density plots. It removes from the plots all genes that have FPKM value lower than this value.",
"sbg:toolDefaultValue": "0.0001",
"inputBinding": {
"prefix": "--densthreshold",
"separate": true,
"sbg:cmdInclude": true
},
"label": "Density plot threshold"
},
{
"sbg:category": "Basic Options",
"type": [
"null",
"boolean"
],
"id": "#thresholds_off",
"description": "Set this parameter in case you don't want to eliminate lower expressed genes on dispersion and density plots. Be aware that this would cause plots to be stretched in order to show these low values for dispersion and FPKM.",
"sbg:toolDefaultValue": "False",
"inputBinding": {
"prefix": "--thresholdsoff",
"separate": true,
"sbg:cmdInclude": true
},
"label": "Turn off thresholds"
}
],
"hints": [
{
"class": "DockerRequirement",
"dockerImageId": "0c4541b52eb7",
"dockerPull": "images.sbgenomics.com/ana_d/cummerbund-qc:2.8.2--1.0"
},
{
"class": "sbg:CPURequirement",
"value": 8
},
{
"class": "sbg:MemRequirement",
"value": 6000
}
],
"sbg:modifiedOn": 1448366962,
"sbg:latestRevision": 0,
"sbg:id": "rfranklin/my-project/cummerbundqc/0",
"sbg:job": {
"inputs": {
"cuffdiff_zip": {
"class": "File",
"size": 0,
"path": "cuffdiff_zip.ext",
"secondaryFiles": []
},
"density_threshold": 0,
"dispersion_threshold": 0,
"thresholds_off": true
},
"allocatedResources": {
"cpu": 8,
"mem": 6000
}
},
"sbg:cmdPreview": "python /opt/cummerbund-qc.py --cuffzip cuffdiff_zip.ext --dispthreshold 0 --densthreshold 0 --thresholdsoff cuffdiff_zip.ext",
"description": "CummeRbundQC assesses the quality of a differential expression analysis performed with Cuffdiff. It accepts differential expression results in the form of a cuffdiff.zip folder as input and produces a report with charts that can be viewed on Seven Bridges platform or downloaded to your local drive. \n\nCummeRbundQC is built on top of CummeRbund v. 2.8.2. CummeRbundQC incorporates the \"Global Statistics and Quality Control\" graphs described in the CummeRbund manual. These visualizations provide an overview of the relationships among the replicates and help in detecting over-dispersion in samples.",
"sbg:links": [
{
"id": "http://bioconductor.org/packages/release/bioc/html/cummeRbund.html",
"label": "Homepage"
},
{
"id": "http://bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf",
"label": "Manual"
},
{
"id": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/",
"label": "Publication"
}
],
"temporaryFailCodes": [],
"successCodes": [],
"sbg:contributors": [
"rfranklin"
],
"label": "CummeRbundQC",
"sbg:sbgMaintained": false,
"baseCommand": [
"python",
"/opt/cummerbund-qc.py"
],
"sbg:createdBy": "rfranklin",
"class": "CommandLineTool",
"sbg:modifiedBy": "rfranklin",
"sbg:validationErrors": [],
"sbg:revisionsInfo": [
{
"sbg:modifiedBy": "rfranklin",
"sbg:modifiedOn": 1448366962,
"sbg:revision": 0
}
],
"sbg:categories": [
"Differential-Expression",
"Plotting-and-Rendering"
],
"arguments": [],
"stdin": "",
"sbg:license": "Artistic License 2.0",
"sbg:createdOn": 1448366962
}
}Copy an app
This call copies the specified app to the specified project. The app should be one in a project that you can access; this could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project.
https://api.sbgenomics.com/v2/apps/{app_id}/actions/copyhttps://eu-api.sbgenomics.com/v2/apps/{app_id}/actions/copyhttps://gcp-api.sbgenomics.com/v2/apps/{app_id}/actions/copyapp_ids
Recall from the apps section in the API overview that the app_id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.
Note that if you omit the revision_number, the API will use the latest app revision.
You can get the app_id for an app by making the call to list all apps available to you
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
app_id
The ID for the app you are querying. It can be obtained by making the call to list all apps available to you
fields
string
Selector specifying a subset of fields to include in the response.
"project"
required
string
The name of the project you want to copy the app to
"name"
string
The new name the app will have in the target project. If its name will not change, omit this key.
"strategy"
string
The method for copying the app (also see the diagram below).
clone- copy all revisions and continue getting updates form the original app (default method when the key is omitted)direct- copy only the latest revision and get the updates from this point onclone_direct- copy the app like the direct strategy, but keep all revisionstransient- copy only the latest revision and continue getting updates from the original app.
POST /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/actions/copy HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl --data '{"project": "RFranklin/my-project", "name": "new app name"}' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/apps/RFranklin/sandbox/delly2-workflow/actions/copy"{
"project": "rfranklin/my-project",
"name": "new app name",
"strategy": "direct"
}This call returns the full Common Workflow Language (CWL) description of the copied app. This is typically a lengthy JSON object; for conciseness, we have not included it here, but made it available on this page.
Get raw CWL for an app
This call returns information about the specified app, as raw CWL. The call differs from the call to get details of an app by returning a JSON object that is the CWL.
The app should be one in a project that you can access. This could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project.
https://api.sbgenomics.com/v2/apps/{app_id}/rawhttps://eu-api.sbgenomics.com/v2/apps/{app_id}/raw https://gcp-api.sbgenomics.com/v2/apps/{app_id}/rawapp_ids
Recall from the apps section in the API overview that the app_id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.
Note that if you omit revision_number, the API will return the latest app revision.
You can get the app_id for an app by making the call to list all apps available to you
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
app_id
The ID for the app you are querying. It can be obtained by making the call to list all apps available to you
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/raw HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/raw"Note that this call returns the full CWL description of the app.
{
"successCodes": [],
"sbg:homepage": "https://github.com/pezmaster31/bamtools/wiki",
"sbg:validationErrors": [],
"sbg:sbgMaintained": false,
"temporaryFailCodes": [],
"requirements": [],
"sbg:latestRevision": 0,
"description": "BamTools Merge merges multiple BAM files into a single file.",
"sbg:job": {
"inputs": {
"region": "chr1",
"input_bam_files": [
{
"path": "1.bam"
},
{
"path": "2.bam"
}
]
},
"allocatedResources": {
"cpu": 1,
"mem": 1000
}
},
"sbg:toolAuthor": "Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg",
"hints": [
{
"dockerImageId": "f808163d4cd3",
"class": "DockerRequirement",
"dockerPull": "images.sbgenomics.com/markop/bamtools:2.4.0"
},
{
"value": 1,
"class": "sbg:CPURequirement"
},
{
"value": 1000,
"class": "sbg:MemRequirement"
}
],
"sbg:copyOf": "djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0",
"sbg:createdOn": 1452181866,
"arguments": [
{
"position": 1,
"prefix": "-out",
"separate": true,
"valueFrom": "merged.bam"
}
],
"outputs": [
{
"sbg:fileTypes": "BAM",
"id": "#output_bam_file",
"outputBinding": {
"glob": "merged.bam",
"sbg:metadata": {},
"sbg:inheritMetadataFrom": "#input_bams"
},
"description": "Output BAM file.",
"type": [
"File"
],
"label": "Output BAM file"
}
],
"sbg:categories": [
"SAM/BAM-Processing"
],
"sbg:contributors": [
"RFranklin"
],
"sbg:links": [
{
"id": "https://github.com/pezmaster31/bamtools",
"label": "Homepage"
},
{
"id": "https://github.com/pezmaster31/bamtools/wiki",
"label": "Wiki"
}
],
"stdout": "",
"stdin": "",
"sbg:project": "RFranklin/my-project",
"inputs": [
{
"sbg:fileTypes": "BAM",
"id": "#input_bam_files",
"inputBinding": {
"sbg:cmdInclude": true,
"prefix": "-in",
"separate": true,
"itemSeparator": null,
"position": 0
},
"description": "The input BAM files.",
"label": "Input BAM files",
"type": [
{
"type": "array",
"items": "File"
}
],
"sbg:category": "Input & Output"
},
{
"id": "#region",
"inputBinding": {
"sbg:cmdInclude": true,
"position": 2,
"separate": true,
"prefix": "-region"
},
"description": "A region of interest (e.g. \"chr1:500..chr3:1500\"). See the documentation for more info.",
"label": "Region of interest",
"type": [
"null",
"string"
],
"sbg:category": "Input & Output"
}
],
"label": "BamTools Merge",
"sbg:createdBy": "RFranklin",
"baseCommand": [
"/opt/bamtools/bin/bamtools",
"merge"
],
"sbg:toolkitVersion": "2.4.0",
"sbg:id": "RFranklin/my-project/bamtools-merge-2-4-0/0",
"sbg:license": "The MIT License",
"sbg:revision": 0,
"sbg:cmdPreview": "/opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1",
"sbg:modifiedOn": 1452181866,
"id": "https://api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/",
"class": "CommandLineTool",
"sbg:modifiedBy": "RFranklin",
"sbg:revisionsInfo": [
{
"sbg:modifiedBy": "RFranklin",
"sbg:modifiedOn": 1452181866,
"sbg:revision": 0
}
],
"sbg:toolkit": "BamTools"
}Add an app using raw CWL
This call allows you to add an app using raw CWL.
https://api.sbgenomics.com/v2/apps/{app_id}/rawhttps://eu-api.sbgenomics.com/v2/apps/{app_id}/rawhttps://gcp-api.sbgenomics.com/v2/apps/{app_id}/rawapp_ids
Recall from the apps section in the API overview that the app_id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.
Note that if you omit the revision_number field, the API will use the latest app revision.
You can create the {app_short_name} for your app when you upload it. It can be any string of alphanumeric characters, with no spaces. Note that the app's given name (a full human-readable string) is contained in the CWL that you POST.
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
Content-Type
Depending on the type of file you are uploading:
application/jsonfor a JSON fileapplication/yamlfor a YAML file
app_id
The ID for the app you are you want to upload. It should reference the project that you want the app to be added to, a short name for the app (containing no non-alphanumeric characters or spaces), and a revision number.
fields
string
Selector specifying a subset of fields to include in the response.
Request body
The body of the request should be a CWL app description saved as a JSON or YAML file. For a template of this description, try making the call to get raw CWL for an app about an app already in one of your projects.
POST /v2/apps/RFranklin/my-project/my-app/raw HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl --data-binary '@my-app.json' -s -H "X-SBG-Auth-Token: 7942f56901534434a054dafc3813bc96" -H "content-type: application/json" -X POST "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/my-app/raw"Get raw CWL for an app revision
This call returns information about the specified app revision, as raw CWL. The call differs from the call to get the details of an app revision by returning a JSON object that is the CWL description of the app revision.
The app should be one in a project that you can access. This could be an app that has been uploaded to the Seven Bridges Platform by a project member, or a publicly available app that has been copied to the project.
https://api.sbgenomics.com/v2/apps/{app_id}/rawhttps://eu-api.sbgenomics.com/v2/apps/{app_id}/rawhttps://gcp-api.sbgenomics.com/v2/apps/{app_id}/rawapp_ids
Recall from the apps section in the API overview that the app_id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.
You can get the app_id for an app by making the call to list all apps available to you
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
app_id
The ID for the app you are querying. It can be obtained by making the call to list all apps available to you
revision number
The integer that is the revision number of the app
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw"{
"successCodes": [],
"sbg:homepage": "https://github.com/pezmaster31/bamtools/wiki",
"sbg:validationErrors": [],
"sbg:sbgMaintained": false,
"temporaryFailCodes": [],
"requirements": [],
"sbg:latestRevision": 0,
"description": "BamTools Merge merges multiple BAM files into a single file.",
"sbg:job": {
"inputs": {
"region": "chr1",
"input_bam_files": [
{
"path": "1.bam"
},
{
"path": "2.bam"
}
]
},
"allocatedResources": {
"cpu": 1,
"mem": 1000
}
},
"sbg:toolAuthor": "Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg",
"hints": [
{
"dockerImageId": "f808163d4cd3",
"class": "DockerRequirement",
"dockerPull": "images.sbgenomics.com/markop/bamtools:2.4.0"
},
{
"value": 1,
"class": "sbg:CPURequirement"
},
{
"value": 1000,
"class": "sbg:MemRequirement"
}
],
"sbg:copyOf": "djordje_klisic/public-apps-by-seven-bridges/bamtools-merge-2-4-0/0",
"sbg:createdOn": 1452181866,
"arguments": [
{
"position": 1,
"prefix": "-out",
"separate": true,
"valueFrom": "merged.bam"
}
],
"outputs": [
{
"sbg:fileTypes": "BAM",
"id": "#output_bam_file",
"outputBinding": {
"glob": "merged.bam",
"sbg:metadata": {},
"sbg:inheritMetadataFrom": "#input_bams"
},
"description": "Output BAM file.",
"type": [
"File"
],
"label": "Output BAM file"
}
],
"sbg:categories": [
"SAM/BAM-Processing"
],
"sbg:contributors": [
"RFranklin"
],
"sbg:links": [
{
"id": "https://github.com/pezmaster31/bamtools",
"label": "Homepage"
},
{
"id": "https://github.com/pezmaster31/bamtools/wiki",
"label": "Wiki"
}
],
"stdout": "",
"stdin": "",
"sbg:project": "RFranklin/my-project",
"inputs": [
{
"sbg:fileTypes": "BAM",
"id": "#input_bam_files",
"inputBinding": {
"sbg:cmdInclude": true,
"prefix": "-in",
"separate": true,
"itemSeparator": null,
"position": 0
},
"description": "The input BAM files.",
"label": "Input BAM files",
"type": [
{
"type": "array",
"items": "File"
}
],
"sbg:category": "Input & Output"
},
{
"id": "#region",
"inputBinding": {
"sbg:cmdInclude": true,
"position": 2,
"separate": true,
"prefix": "-region"
},
"description": "A region of interest (e.g. \"chr1:500..chr3:1500\"). See the documentation for more info.",
"label": "Region of interest",
"type": [
"null",
"string"
],
"sbg:category": "Input & Output"
}
],
"label": "BamTools Merge",
"sbg:createdBy": "RFranklin",
"baseCommand": [
"/opt/bamtools/bin/bamtools",
"merge"
],
"sbg:toolkitVersion": "2.4.0",
"sbg:id": "RFranklin/my-project/bamtools-merge-2-4-0/0",
"sbg:license": "The MIT License",
"sbg:revision": 0,
"sbg:cmdPreview": "/opt/bamtools/bin/bamtools merge -in 1.bam -in 2.bam -out merged.bam -region chr1",
"sbg:modifiedOn": 1452181866,
"id": "https://api.sbgenomics.com/RFranklin/my-project/bamtools-merge-2-4-0/0/raw/",
"class": "CommandLineTool",
"sbg:modifiedBy": "RFranklin",
"sbg:revisionsInfo": [
{
"sbg:modifiedBy": "RFranklin",
"sbg:modifiedOn": 1452181866,
"sbg:revision": 0
}
],
"sbg:toolkit": "BamTools"
}Get details of an app revision
This call allows you to obtain a particular revision of a tool, which is not necessarily the most recent version.
https://api.sbgenomics.com/v2/apps/{app_id}/{revision_number}https://eu-api.sbgenomics.com/v2/apps/{app_id}/{revision_number}https://gcp-api.sbgenomics.com/v2/apps/{app_id}/{revision_number}app_ids
Recall from the apps section in the API overview that the app_id has the form {project_owner}/{project}/{app_short_name}/{revision_number}.
You can get the app_id for an app by making the call to list all apps available to you
X-SBG-Auth-Token
required
Your Seven Bridges Platform authentication token.
app_id
The ID for the app you are querying. It can be obtained by making the call to list all apps available to you
revision_number
The integer denoting the revision of the app.
fields
string
Selector specifying a subset of fields to include in the response.
GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0 HTTP/1.1
Host: api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw"{
"href": "https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/RSEM BAM2WIG/4",
"id": "admin/sbg-public-data/rsem-bam2wig-1-2-31/4",
"project": "admin/sbg-public-data",
"name": "RSEM BAM2WIG",
"revision": 4,
"raw": {
"id": "https://api.sbgenomics.com/v2/apps/admin/sbg-public-data/rsem-bam2wig-1-2-31/4/raw/",
"sbg:modifiedOn": 1476979693,
"inputs": [
{
"description": "Can be either in SAM/BAM/CRAM format. Must be sorted.",
"label": "Sorted alignment file",
"type": [
"File"
],
"sbg:fileTypes": "BAM, SAM, CRAM",
"inputBinding":
{ "position": 0, "separate": true, "sbg:cmdInclude": true },
"sbg:stageInput": "copy",
"id": "#sorted_alignment_file"
},
{
"description": "If this is set, RSEM will not look for “ZW” tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM.",
"label": "No fractional weight",
"sbg:category": "Options",
"type": [
"null",
"boolean"
],
"id": "#no_fractional_weight",
"inputBinding":
{ "prefix": "--no-fractional-weight", "position": 3, "separate": true, "sbg:cmdInclude": true },
"sbg:toolDefaultValue": "off"
}
],
"sbg:cmdPreview": "rsem-bam2wig /path/to/aligned_file.bam aligned_file.wiggle_plot.wig aligned_file.wiggle_plot",
"sbg:latestRevision": 4,
"sbg:revisionsInfo": [
{ "sbg:revisionNotes": null, "sbg:revision": 0, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": null, "sbg:revision": 1, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": null, "sbg:revision": 2, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": "Updated description.", "sbg:revision": 3, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
,
{ "sbg:revisionNotes": null, "sbg:revision": 4, "sbg:modifiedOn": 1476979693, "sbg:modifiedBy": "admin" }
],
"hints": [
{ "value": 1, "class": "sbg:CPURequirement" }
,
{ "value": 1000, "class": "sbg:MemRequirement" }
,
{ "dockerImageId": "67d3a6c01e92210f43c8ef809c2a245a75bf7d5a52762823cdc3b2e784de576c", "class": "DockerRequirement", "dockerPull": "images.sbgenomics.com/uros_sipetic/rsem:1.2.31" }
],
"stdin": "",
"sbg:links": [
{ "label": "RSEM Homepage", "id": "http://deweylab.github.io/RSEM/" }
,
{ "label": "RSEM Source Code", "id": "https://github.com/deweylab/RSEM" }
,
{ "label": "RSEM Download", "id": "https://github.com/deweylab/RSEM/archive/v1.2.31.tar.gz" }
,
{ "label": "RSEM Publications", "id": "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323" }
,
{ "label": "RSEM Documentation", "id": "http://deweylab.github.io/RSEM/README.html" }
],
"stdout": "",
"description": "RSEM BAM2WIG generates a wiggle plot representing the expected number of reads overlapping each position in the genome/transcript from the sorted genome/transcript BAM file output.\n\n###Common issues###\nNone",
"sbg:validationErrors": [],
"sbg:image_url": null,
"sbg:toolkitVersion": "1.2.31",
"sbg:toolkit": "RSEM",
"requirements": [
{
"id": "#cwl-js-engine",
"class": "ExpressionEngineRequirement",
"requirements": [
{ "class": "DockerRequirement", "dockerPull": "rabix/js-engine" }
]
}
],
"sbg:id": "admin/sbg-public-data/rsem-bam2wig-1-2-31/4",
"sbg:categories": [
"Converters",
"Plotting-and-Rendering",
"RNA"
],
"sbg:toolAuthor": "Bo Li, Colin Dewey",
"temporaryFailCodes": [],
"label": "RSEM BAM2WIG",
"sbg:createdBy": "admin",
"class": "CommandLineTool",
"sbg:project": "admin/sbg-public-data",
"sbg:sbgMaintained": false,
"sbg:revision": 4,
"baseCommand": [
"rsem-bam2wig"
],
"sbg:contributors": [
"admin"
],
"sbg:createdOn": 1476979693,
"successCodes": [],
"sbg:modifiedBy": "admin",
"sbg:license": "GNU General Public License v3.0 only",
"arguments": [
{
"position": 1,
"valueFrom": {
"engine": "#cwl-js-engine",
"script": "{\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\n x = \"\"\n for (i=0; i<str.length-1; i++) {\n if (i<str.length-2)
{\n x = x + str[i] + '.'\n } else {\n x = x + str[i]\n }\n }\n return x + \".wiggle_plot.wig\"\n}",
"class": "Expression"
},
"separate": true
},
{
"position": 2,
"valueFrom": {
"engine": "#cwl-js-engine",
"script": "{\n var str = $job.inputs.sorted_alignment_file.path.split('/').pop().split('.')\n x = \"\"\n for (i=0; i<str.length-1; i++) {\n if (i<str.length-2) {n x = x + str[i] + '.'n }
else
{\n x = x + str[i]\n }
\n }\n return x + \".wiggle_plot\"\n}",
"class": "Expression"
},
"separate": true
}
],
"outputs": [
{
"description": "Output wiggle file.",
"label": "Output wiggle file",
"type": [
"null",
"File"
],
"sbg:fileTypes": "WIG",
"outputBinding":
{ "glob": "*.wig", "sbg:inheritMetadataFrom": "#sorted_alignment_file" }
,
"id": "#rsem_bam_to_wiggle_plot_file"
}
],
"sbg:job": {
"allocatedResources":
{ "mem": 1000, "cpu": 1 }
,
"inputs": {
"no_fractional_weight": false,
"sorted_alignment_file":
{ "size": 0, "path": "/path/to/aligned_file.bam", "secondaryFiles": [], "class": "File" }
}
}
}
}Add an app revision using raw CWL
This call creates a new revision for an existing app. It adds a new CWL app description, and stores it as the named revision for the specified app.
https://api.sbgenomics.com/v2/apps/{app_id}/rawhttps://eu-api.sbgenomics.com/v2/apps/{app_id}/raw