Specifying locations of inputs, outputs and exports

The location of input data for an analysis, and the locations to save outputs or export results to, are specified using URLs. CLC URL types are described at the top of the help returned when the clcserver command is run with an incomplete set of arguments. Information about CLC URLs is also provided in a table below.

Where a CLC URL is expected as the value for a parameter, the type is specified in the help for relevant parameters. For example, running the following command: 

	clcserver -S <server> -U <username> -W <password or token> -A assemble_sanger_sequences

would result in help text being printed to screen that included the following: 

	-i, --input <ClcObjectUrl>
	-d, --destination <ClcServerObjectUrl>

For CLC Object URLs, there are 2 forms:


Table 6.1: CLC URL types
CLC URL type Used for URL forms) Details and Examples)
ClcServerObjectUrl
ClcObjectUrl 		Files and folders in CLC Server
file locations. 		clc://server/
clc.//host:port
Name form examples:
clc://server/CLC_Server_Loc/path/to/myreads
clc://host01:7777/CLC_Server_Loc/path/to/myreads
ID form examples:
clc://server/3123-2131uafd-sads/213-sddsa123-5232
clc://host01:7777/3123-2131uafd-sads/213-sddsa123-5232
ClcFileUrl Files and folders in CLC Server
import/export directories 		clc://serverfile/ Full path to file in a CLC Server import/export directory.
Example:
clc://serverfile/full/path/to/impexpdir/reads/Fwd4_R1.fastq
If direct data transfer from client systems has been enabled for the CLC Server, a full path to a file on the local file system can be provided.
ClcCloudFileUrl Files and folders in internet locations clc://cloudfile/ or URLs Examples:
clc://cloudfile/s3://my-bucket/reads/Fwd4_R1.fastq
s3://my-bucket/reads/Fwd4_R1.fastq
https://www.dropbox.com/1u1sxo/Fwd4_R1.fastq


Information about providing inputs to workflows being run on the CLC Server Command Line Tools are provided in Providing input data for analyses on a CLC Server.

Using data stored on AWS S3 as input

Data on S3 specified as input for an analysis on the CLC Server is downloaded to the CLC Server at the start of the analysis. Note that AWS charges for data download.

Data can be analyzed directly on AWS, with results saved to AWS S3, using CLC Genomics Cloud setup. Please refer to the CLC Cloud Module for further information about this: https://resources.qiagenbioinformatics.com/manuals/clccloudmodule/current/index.php?manual=Overview_CLC_Genomics_Cloud.html.

Exporting results

Data can be exported to compatible formats using an export command or using workflows containing export elements. The location to save the exported file to is specified using a ClcFileURL, ClcCloudFileUrl or AWS S3 URL.

Note that when an export is run on the CLC Server Command Line Tools and exported to AWS S3, the exported file will be placed in a subfolder of the specified location with a name made up of a combination of the export file name and a unique string. This is to avoid the danger of overwriting existing files.

Further information about exporting results from workflows is in Saving workflow outputs and exporting results.


Subsections