!!! Large parts of this section is DEPRECATED. We are now using the Slim version in the Slim folder !!!

qmrl_mtb

Pipeline for mtb analysis built for qmrl. A full list of installed tools are listed below.

Please report bugs in Issues, some software are undergoing transitions from Java8 to Java11, which requires updating of the Dockerfile. I require community feedback to alert me as I am not a regular user of this docker.

Manual Instructions

Written for debian-based OS. May work on similar architectures with no or minor syntax tweaks.

Pull cloud build. (Not always reliable, cloud build tends to fail for such a large image.=)

1. Set up and log in to your docker account if you haven't https://www.docker.com/
2. Pull the image with docker pull dockersubtest/qmrl_mtb
3. Make a shared directory, such as mkdir ~/dhost_mount
4. Run the docker with docker run -it -p 5900:5900 -p 8787:8787 -v $HOME/dhost_mount:/dcont_mount/ qmrl_mtb /bin/bash

Local build

1. Set up and log in to your docker account if you haven't https://www.docker.com/
2. Ensure git is installed
3. Clone this git project git clone https://github.com/Firedrops/qmrl_mtb.git and navigate to the folder (usually ~/qmrl_mtb/)
4. Build the image sudo docker build -t qmrl_mtb .
5. Wait... build is expected to take about 2 hours with a docker image ~40 GB.
6. Make a shared directory, such as mkdir ~/dhost_mount
7. Run the docker with docker run -it -p 5900:5900 -p 8787:8787 -v $HOME/dhost_mount:/dcont_mount/ qmrl_mtb /bin/bash

To save a local copy of the image (e.g. thumbdrive)

1. To save: sudo docker save -o <path to directory>/qmrl_mtb.docker qmrl_mtb
2. To load: sudo docker load -i <path to directory>/qmrl_mtb.docker Please take care to update docker run parameters accordingly (e.g. path of the shared directory)

To use the GUI

1. Ensure you have a VNC client installed on the host machine (e.g. Remmina)
2. Start the VNC server from within the docker vncserver $DISPLAY -geometry 1920x1080
3. In your VNC client, select VNC protocol and connect to localhost:5900 The password is simply password.

To switch Java versions

In the docker, use update-alternatives --config java

To access NeCTAR

Simply use the ssh protocol as usual.

To exit the container (e.g. shut it down)

Simply enter exit command or ctrl + c.

To leave the container without stopping it

Analogous to tabbing out to another window and letting it continue running in the background.

1. ctrl + p or ctrl + q
2. To attach back, docker ps (may have to add sudo), note the first 3 characters under ID. For example, JHD898A. 2 will be sufficient if you only have 1 or a few docker containers running, without ID overlaps.
3. docker attach <ID>. For example docker attach JHD.

This is not recommended. Consider simply by running another terminal window on the host machine if possible.

To pass files in/out from host to docker

This can be useful for easily passing scripts, source files, and output files in/out of the docker. Simply move/copy them into ~/dhost_mount (host-side), and /dcont_mount/ (docker-side). Note that the host is in home, and docker in root.

IMPORTANT! Only files stored to /dcont_mount/ directory in the docker will be persistent. All other files will be lost on termination of docker.

To use R (deprecated, can be used via VNC, but this method should still work)

1. Run any internet browser on your host machine.
2. Navigate to http://localhost:8787. Further documentation can be found here

Auto Instructions (Not yet functional)

Written for debian-based OS. May work on similar architectures with no or minor syntax tweaks.

1. Set up a docker account if you haven't https://www.docker.com/
2. Ensure git is installed
3. Clone this git project git clone https://github.com/Firedrops/qmrl_mtb.git and navigate to the folder (usually ~/qmrl_mtb/)
4. Open duser.txt, dpass.txt, and lpass.txt. Replace placeholder text with your docker username, docker password, and linux password, respectively.
5. Optional: In case your working directory is not ~/qmrl_mtb/, open and edit the first few lines of init.sh to match your working directory.
6. Run init.sh. init.sh checks for existing docker installation, and installs it automatically if it is not found, and logs in to docker, and pulls the qmrl_mtb docker image, and creates a directory ~/dhost_mount to share files in/out of the docker, and runs and and attaches user input into the docker image. At this point (you can see when your user input becomes [email protected]) you are inside the docker, and can use its tools.

Tools included in this docker

Bcftools

Beast 1 and 2

Bedtools

Bwamem

Canu

Circos

Circulator

FastQC

Figtree

Freebayes

Gatk

IGV

Kraken

MEGA

MTBseq

Minimap2

Mummer (and Yaggo)

Mykrobe predictor

Picardtools

Pilon

Quast

R/R-Studio

RAxML

Racon

Rapiddr

Samtools

SnpEFF/snpSIFT

Spades

TempEst

Trimal

Trimmomatic