AWS Batch command with no spaces?

user_1761521 0
Viewed 90

I have a command I am trying to run, minimus2 <prefix> -D OVERLAP=100 -D MINID=95 -D THREADS=1 and there can be no spaces for the -D commands, e.g. minimus2 <prefix> -D OVERLAP 100 -D MINID 95 -D THREADS 1, will fail.

I've tried,

"Command":[
  "minimus2",
  "Ref::afgPrefixFile",
  "-D",
  "OVERLAP=",
  "Ref::overlap",
  "-D",
  "MINID=",
  "Ref::minid",
  "-D",
  "THREADS=",
  "Ref::threads"
]

which returns minimus2 <prefix file> -D OVERLAP= 100 -D MINID= 95 -D THREADS= 1, this will add a space after the = and causes the command to fail. And,

"Command":[
  "minimus2",
  "Ref::afgPrefixFile",
  "-D",
  "OVERLAP=Ref::overlap",
  "-D",
  "MINID=Ref::minid",
  "-D",
  "THREADS=Ref::threads"
]

Which doesn't work. How can I build an AWS Batch command where some parameters don't generate spaces?

aws-batch amazon-web-services
1 Answers

Not ideal I know, but you could set your parameters to the whole string? For example:

"parameters" : {"overlap" : "OVERLAP=THE_VALUE", ....}
user_1222010
Related