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.
$ 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 /email@example.com/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 /firstname.lastname@example.org/home/MinhashDev Name Owner Type Moddate Size User perm Global perm UC.MICU.02.30.msh email@example.com job_result 2016-10-01T03:04:01 1513 o n .UC.MICU.02.30.msh firstname.lastname@example.org folder 2016-10-01T01:19:34 0 o n UC.MICU.02.30.fastq email@example.com 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).