mRNASeq on Emory AWS tutorial

1. connect to Emory VPN (BIG-IP)

2. FTP FASTQ files to 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. change permission of the log file to allow subsequent tki calls

> chmod g+w /mnt/efs/bin/emory-tki/logs/tkiclient.log

6. clone the mRNAseq pipeline
> git clone --branch aws https://github.com/sekalylab/mRNASeq.git

7. launch the mRNASeq pipeline
> bash mRNA.preprocess_master.sh -d /mnt/efs/myDirectoryName

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

9. empty the EFS storage
> rm -r /mnt/efs/myDirectoryName