Uploading data from the command line into your workspace

The PATRIC workspace is a place where you can upload your data so that it can be integrated with existing public data in PATRIC while at the same time maintaining privacy. As an example, you can upload contigs to your workspace, annotate them using the PATRIC annotation service, and then compare the annotated results with publicly annotated genomes in PATRIC.

In this example, I am going to upload contigs from my mac to my workspace in PATRIC using the command line interface rather than using the web interface for uploading contigs to my workspace.

Uploading data

The ws-create command is used to upload data to my workspace:
$ ws-create -h
ws-create.pl [-ahopu] [long options...]   
	     -p --permission   Permissions for folders created
	     -u --useshock     Upload file to shock and store link in workspace
	     -o --overwrite    Overwrite existing destination object
	     --wsurl           Workspace URL
	     -a --admin        Run as administrator
	     -h --help         Show this usage message
$ ws-create -u /brettin@patricbrc.org/home/MinhashDev/UC.MICU.02.30.fastq Reads /home/brettin/assemblies/UC.MICU.02.30.fastq

In this case, I used the -u option to tell the system to upload the genomes into the Shock bulk storage system; for any file larger than a few kilobytes we recommend that this option be used.

If I want to verify the uploaded reads, I can use do a listing on the folder that I uploaded the reads to.

$ ws-ls /brettin@patricbrc.org/home/MinhashDev

Name                Owner                 Type       Moddate             Size       User perm Global perm
UC.MICU.02.30.msh   brettin@patricbrc.org job_result 2016-10-01T03:04:01       1513 o         n          
.UC.MICU.02.30.msh  brettin@patricbrc.org folder     2016-10-01T01:19:34          0 o         n          
UC.MICU.02.30.fastq brettin@patricbrc.org reads      2016-09-30T21:34:12 8284314281 o         n    

The folder listing includes fields such as owner, the object's name (specified by first positional argument in the ws-create command) type (specified by the second positional argument) and permissions (specified by the third positional argument).