Get details of an app revision

/apps/{app_id}/{revision_number}

This call allows you to obtain a particular revision of a tool, which needn't be the most recent version.

Path

https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/apps/{app_id}/{revision_number}

👍

app_ids

Recall from 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

Request

Example request

HTTP

GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0 HTTP/1.1
Host: api.sb.biodatacatalyst.nhlbi.nih.gov
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74

cURL

curl  -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw"

Header Fields

Name	Description
X-SBG-Auth-Token required	Your authentication token.

Path parameters

Name	Description
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.

Query parameters

Name	Data type	Description
fields	string	Selector specifying a subset of fields to include in the response.

Response

See a list of response codes that may be contained in the body of the response.

Example response body

JSON

{
	"href": "https://api.sb.biodatacatalyst.nhlbi.nih.gov/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.sb.biodatacatalyst.nhlbi.nih.gov/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": "123456c01e92210f43c8ef809c2a245a75bf7d5a52762823cdc3b2e784de576c", "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" }
}
}
}
}