Get details of an app revision

/apps/{app_id}/{revision_number}

For general information on the API, including formatting, parameters, and pagination, please see the API Overview.

This call allows you to obtain a particular revision of a tool, which is not necessarily the most recent version.

https://cavatica-api.sbgenomics.com/v2/apps/{app_id}/{revision_number}

๐Ÿ‘

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

GET /v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0 HTTP/1.1
Host: cavatica-api.sbgenomics.com
X-SBG-Auth-Token: 3259c50e1ac5426ea8f1273259740f74
curl  -s -H "X-SBG-Auth-Token: 6282d5e2121d43e7900e9d52b15845e7" -H "content-type: application/json" -X GET "https://cavatica-api.sbgenomics.com/v2/apps/RFranklin/my-project/bamtools-merge-2-4-0/0/raw"

Header Fields

NameDescription
X-SBG-Auth-Token
required
Your CAVATICA authentication token.

Path parameters

NameDescription
app_idThe ID for the app you are querying. It can be obtained by making the call to list all apps available to you
revision_numberThe integer denoting the revision of the app.

Query parameters

NameData typeDescription
fieldsstringSelector specifying a subset of fields to include in the response.

Response

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

Example response body

{
	"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 โ€œZWโ€ 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": "67d3a6c01e91234f43c8ef809c2a245a75bf7d5a52762823cdc3b2e784de576c", "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" }
}
}
}
}

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