Shock Clients

Command Line Client

Make sure the shock-client command is in your path. You will also need access to a running shock server. For demo purposes, I've installed the shock server on localhost. See installing.

1. Set up your .shock-client.cfg file in your home directory. The only changes that I had to make to the template was set the server url.

The url requires the protocol (http) and port (7044).

[server] url=http://localhost:7044

2. Authenticate with shock server. For this I'm using the Globus Online

shock-client auth show shock-client set

3. Upload some data.

For this example, I have ChIP-seq data. I have two files, Input_tags.bed and Treatement_tags.bed. The first is the control and the second represents a treatment. These files are used as in put into the MACS program which computes transcription factor binding sites.

In total, we will create three shock nodes. One node holding the meta-data and data for the control data represented in the Input_tags.bed file. The second node holding the meta-data and data for the treatment data in the Treatment_tags.bed file. The third node is a virtual node used to link the two preceding nodes.

shock-client create -attribute=input_tags.json -full=Input_tags.bed

The input parameters must have an = sign. Omitting the equal sign can cause unexpected and uninformative error messages.

This returns the node id in a json document. Here is the output json document:

{ "id": "546955d9-d8a0-484c-9dd6-639be14ff4ea", "version": "b6b51c4b26704c9544a870d079fb435f", "file": { "name": "Input_tags.bed", "size": 156714470, "checksum": { "md5": "74394f5fcb0b2b5ff73d5fc1f3cd599b", "sha1": "2385e57e8edec916902d29f654ca05f5abcc301e" }, "format": "", "virtual": false, "virtual_parts": null }, "attributes": { "type": "control" }, "indexes": { "size": { "total_units": 150, "average_unit_size": 1048576 } }, "tags": null, "linkages": null }

4. Download that data.