How to use the pipeline in the docker container¶

docker pull mwakok/satay:latest

docker build . -t mwakok/satay:latest

Run the pipeline¶

Move to the location where you have the data you would like to mount to the container , to use $(pwd) in the command bellow (simplest option) , otherwise indicate the absolute path from your computer you would like to be loaded.

# For Windows (and WSL):
docker run --rm -it -e DISPLAY=host.docker.internal:0 -v /$(pwd):data/ mwakok/satay:latest 

# For macOS
docker run --rm -it -e DISPLAY=docker.for.mac.host.internal:0 -v $(pwd):/data mwakok/satay 

# For Linux
docker run --rm -it --net=host -e DISPLAY=:0 -v $(pwd):/data mwakok/satay

# For Windows (and WSL):
docker run --rm -it -e DISPLAY=host.docker.internal:0 -v /$(pwd):data/ mwakok/satay:latest bash

# For macOS
docker run --rm -it -e DISPLAY=docker.for.mac.host.internal:0 -v $(pwd):/data mwakok/satay bash

# For Linux
docker run --rm -it --net=host -e DISPLAY=:0 -v $(pwd):/data mwakok/satay bash

The flag -e enables viewing of the GUI outside the container via the Xserver
The flag -v mounts the current directory (pwd) on the host system to the data/ folder inside the container

To know the adapters sequence , one way is to look for the overrepresented sequences in your dataset. Steps:

Run the pipeline with the
- [x] Quality checking raw data CHECKED
- [x] Quality check interrupt CHECKED
When the GUI ask you to continue , say NO and go to your local /data/fastqc_out/
- Open the corresponding html file and go to the “Overrepresented sequences” section
- Copy the sequence that has more than 15% of representation.
Create the adapterfile.fa in your local data folder
- Open a bash terminal and move to the location where you have the data you would like to mount in the pipeline (fastq files)
```
cd /data
```
- Create the adapterfile file customized to your dataset.
```
nano adapterfile.fa
```
- Inside the nano editor , edit the file as follows:
```
> \> Sequence1
>
> Overrepresented sequence 1
>
> \> Sequence2
>
> Overrepresented sequence 2
```
- Ctrl-O save , Ctrl-X and quit the editor
Note

Note to not put empty lines in the text file, otherwise BBDuk might yield an error about not finding the adapters.fa file.!
Run again the container and it will automatically look for that file (adapterfile.fa) in the data folder .

When running the container , mainly for the 1st time , after a reboot of your PC, this may pops up:

Gtk-WARNING **: cannot open display: :0

There is a solution in Linux is typing the following command in the terminal : xhost +