wcc_pdbbind_data

Make alias to Docker. Point to the folder where the pdbbind data is.

alias drd='docker run -ti --rm -p 8888:8888 -v "${HOME}/software/wcc_pdbbind_data":/home/jovyan/work --name rdock $USER/rdock'

Then write commands for list with 5 PDB

# Make standard with 3 runs
drd bash 00_execute_pdb_list.sh -p 00_5_pdb.txt

# With 5 runs 
drd bash 00_execute_pdb_list.sh -p 00_5_pdb.txt n 5

# With 5 runs, and force write -w and force execute -w
drd bash 00_execute_pdb_list.sh -p 00_5_pdb.txt -w -e n 5

drd bash 00_execute_pdb_list.sh -p 00_all_pdb.txt -w -e n 20

Then execute commands with GNU parallel

drd bash commands_run.sh

Get the timings

drd bash 10_get_timings.sh -p 00_all_pdb.txt

Clean up files

drd bash 11_clean_files.sh -p 00_5_pdb.txt
drd bash 11_clean_files.sh -p 00_all_pdb.txt

Run docker image on google cloud

Create VM

create
- Region: europe-west1 (Belgium)
- Zone: europe-west1-b
- Machine type: n1-highcpu-4 (80$/mo)
- Container: Yes, deploy a container image
- Container image: tlinnet/rdock
- Standard persistent disk: 50 GB
- Allow HTTP traffic: Yes
- Allow HTTPS traffic: Yes
- Management, disks, networking, SSH keys
  - Add from $HOME/.ssh/id_rsa.pub
- Preemptibility: On (Price drops 70% down!)
- Startup script (Optional)

#! /bin/bash apt-get update apt-get install -y tmux

SSH to box

EXTIP=35.195.xxx.xxx

ssh $USER@$EXTIP

Inspect docker

The system will automatically start downloading the image. Until completed, this will be shown

docker ps

CONTAINER ID IMAGE                   
8e40cf2035bd gcr.io/gce-containers/konlet:v.....

Stop running image

Inspect

docker images
docker ps -a

#stop all containers:
docker kill $(docker ps -q)

#remove all containers
docker rm $(docker ps -a -q)

Run Jupyter Notebook

Use this alias

alias drd='docker run -ti --rm -p 80:8888 -v "${HOME}/wcc_pdbbind_data":/home/jovyan/work --name rdock tlinnet/rdock'

Then run it

drd

Then in terminal will be

Copy/paste this URL into your browser when you connect for the first time,
to login with a token:
    http://localhost:8888/?token=1e82844a251f85aceb6e868e6806d760d9d9b257c77b6348

In a webbrowser, write (without https, just http)

35.195.xxx.xxx/?token=1e82844a251f85aceb6e868e6806d760d9d9b257c77b6348

Attach to a running Docker

Use this alias

alias drd='docker run -ti --rm -p 80:8888 -v "${HOME}/wcc_pdbbind_data":/home/jovyan/work --name rdock tlinnet/rdock'

Then run bash

drd bash

Open another terminal

ssh $USER@$EXTIP

docker ps
docker attach rdock
docker attach f9479cca9e9e

Ctrl+p, Ctrl+q will turn interactive mode into daemon mode.

Get data

cd $HOME
git clone https://github.com/tlinnet/wcc_pdbbind_data.git
sudo chgrp -R 100 wcc_pdbbind_data
sudo chmod -R g+w wcc_pdbbind_data

# sudo chown -R 1000:100 wcc_pdbbind_data
#sudo chown -R tlinnet:tlinnet wcc_pdbbind_data

Run it

drd bash 00_execute_pdb_list.sh -p 00_5_pdb.txt n 5

drd bash commands_run.sh