Allow use of command and script flags at the same time?

[slagelwa]

I have a pretty complicated command that I want to run on a number of files, each on their own vm. So I put the command in a bash script and I put my file names in a tsv file. What I wanted to run was:

dsub --tasks myfiles --script ./messycmd --command './messycmd $FILE'

However dsub doesn't currently allow you to provide both a script and a command. I can always whip up a docker with my script in it and run it that way, but it just seems kinda unnecessary.

[wnojopra]

Hi @slagelwa,

I might be misunderstanding something, but I'm not sure why you'd need both --command and --script options. You should be able to call your complicated command in its entirety in your script. Within your script, you are able to reference the $FILE for the task. You may find this doc on scripts and commands helpful. There is also an example available here that runs a complicated script on multiple files, each on its own vm.

[slagelwa]

Your correct I can, but I'd rather my script read its input from a command line argument vs. having an embedded environment variable. That way if I want I can run it from the command line instead of as a dsub job. I understand I can set the environment variable and run it, but that's a little more unorthodox.