mRNASeq on Emory AWS tutorial

1. connect to Emory VPN (BIG-IP)

2. FTP FASTQ files on EFS storage

   sftp -i userName.pem username@10.65.122.170  
   cd /mnt/efs
   mkdir myDirectoryName  
   cd myDirectoryName  
   put *.fq.gz  

3. connect to frontend machine
   ssh -i *userName*.pem *username*@10.65.122.170

4. create temporary AWS CLI credentials
   tki
Username: *emoryUserName*
Password: *emoryPassword*
Available Duo Authentication Methods: 1.auto
Available Regions: 2:us-east-2

   Accept the push/sms/phone call.
   This will create AWS CLI credentials valid for 12h (in $HOME/.aws/credentials).

5. clone the mRNAseq pipeline
   git clone https://github.com/sekalylab/mRNASeq.git

6. launch the mRNASeq pipeline
   bash mRNA.preprocess_master.sh -d /mnt/efs/*myDirectoryName*

7. download the output files on local machines
   sftp -i *userName*.pem *username*@10.65.122.170
cd /mnt/efs*myDirectoryName*
get *_genecounts

8. empty the EFS storage
   rm -r /mnt/efs/*myDirectoryName*