Arima Oncology Pipeline

Transfer files

1. cd /mnt/my-volume-huge/ 2.screen

2. wget "https://filetransfer.mdc-berlin.de/?u=aGAfkWwg&p=P2k7zjZU&path=/221202_A00643_0600_BHK53TDSX5_P1574/...."

3. ssh -i id-rsa [email protected]

4. create new screen by this command screen -s arima_screen_name, if you want to check result you have to go in screen

   1. screen -ls - list of screen
   2. screen a

5. docker ps - get list of running docker and take docker id to enter

6. docker exec -it {docker_id} bash - enter inside of docker

7. move R1, R2 to the /Oncology/INPUT/ mv /shared_folder/...R1..fastq.qz /Oncology/INPUT/

8. then run this command when you are in /Oncology folder

bash run_Arima-Oncology-Pipeline-singularity-v0.3.sh -I /Oncology/INPUT/P1574_DNA_01_DHL4_HiChIP_S1_R1_001.fastq.gz,/Oncology/INPUT/P1574_DNA_01_DHL4_HiChIP_S1_R2_001.fastq.gz -o /Oncology/OUTPUT/

7.After running ctrl+a+d

##Checking the screens screen -list screen -r -id If you see the job is done you can move the output folder to the shared folder.

How can I move folders?

1. ssh -i id-rsa [email protected]
2. check job is done or not
   1. screen -list - to get id and
   2. screen -r {id of screen}
   3. if you see job is finished, you can start doing step 4, otherwise use ctrl+a+d to deattach from screen, and job will continue in background
3. move OUTPUT folder to the shared folder in docker

mv /Oncology/OUTPUT/ /shared_folder/OUTPUT/Farage/

5. clean OUTPUT folder

rm -rf /Oncology/OUTPUT

6. then close screen by using exit command multiple times until you exit ssh

Kill Screen

screen -X -S[session # you want to kill] quit

How to check if the job is done?

1. ssh -i id-rsa [email protected]
2. use htop, and if CPU usage is high, it means that job is still running in background.

How to create new docker with host network

docker run -it --network host -v /home/cloud/shared_folder/:/shared_folder/ --name arima_oncology --privileged arimaxiang/arima_oncology:0.3

How to install singularity in docker, (it should be installed in docker)

https://stackoverflow.com/a/66978973

Download .sif file

(it would be better to download file in host server not in docker)

wget ftp://ftp-arimagenomics.sdsc.edu/pub/ARIMA_Oncology_Pipeline/Arima-Oncology-Pipeline-singularity-v0.2.sif shared_folder

Run Mapping inside the docker

bash run_Arima-Oncology-Pipeline-singularity-v0.3.sh -I /Oncology/INPUT/P1574_DNA_01_DHL4_HiChIP_S1_R1_001.fastq.gz,/Oncology/INPUT/P1574_DNA_01_DHL4_HiChIP_S1_R2_001.fastq.gz -o /Oncology/OUTPUT/