[StarCluster] put command bug

[Sagar Chhangawala]

Hi,

I am trying to use put command to transfer a folder containing 
directories and files. However, the recursion is not handled very well. 
The directories are transfered and then the files are put into the 
previously transfered directories instead of outside. I hope the below 
example explains the probelm. Is there a solution for this?

I am using put command as following:

starcluster put -u ubuntu mycluster /home/sagar/Documents/amazon_run/* 
/home/ubuntu/scratch/RNA_run/

My directory listing:
genomes\
get_bam.time
Mock_R1.fastq
Mock_R2.fastq
MO_R1.fastq
MO_R2.fastq
nohup.out
put.time
run_amazon.sh
run_amazon.sh~
run_star.sh
run_star.sh~
run.time
STAR
transcriptome\

The layout of resulting directory on amazon:
/home/ubuntu/scratch/RNA_run/genomes/bwt2/:

get_bam.time
Mock_R1.fastq
Mock_R2.fastq
MO_R1.fastq
MO_R2.fastq
nohup.out
put.time
run_amazon.sh
run_amazon.sh~
run_star.sh
run_star.sh~
run.time
STAR
transcriptome\