Output File Refactors + AWS Scripts

[sstevenshang]

This in PR:

1. Refactored arg parser of SPMAEL module.
2. Added various helper functions to help write/delete files from HDFS (adapted to AWS S3 as well).
3. Added scripts to automate AWS operations (see aws/deploy_to_s3.sh and aws/run_in_emr.sh).

This should close the following issues:

• https://github.com/ncsa/Genomics_EpiQuant/issues/8
• https://github.com/ncsa/Genomics_EpiQuant/issues/12

Note:

• The new file aws/genomics-epiquant-beta-keypair.pem is the key-pair file used for SSH-ing into the EMR cluster. Keep this here in this repo for now. But should be deleted in the future for best practice.

[sstevenshang]

Sounds good. I made some updates:

• Deleted the key pair.
• Changed default sparkMaster to "local".
• Changed it to throw error when output directory exists.

I've tested and verified that this works on local machines. Should be ready to merge