Solutions

2. Download the data

The example fastq file(s) can be downloaded with the following commands.

wget https://introduction-containers.s3.eu-central-1.amazonaws.com/ecoli_reads.tar.gz
tar -xzvf ecoli_reads.tar.gz

3. Manage file ownership while bind mounting a local directory

Exercises

3.1 Run a docker container and approach it interactively. In addition, mount the directory containing the data to /data within the Docker container quay.io/biocontainers/fastqc:0.11.9--0.

  • docker run --rm -it -v $(pwd)/data/:/data quay.io/biocontainers/fastqc:0.11.9--0 /bin/bash

Warning

Don’t mount a directory that contains a lot of files or subdirectories (like ~)

3.2 Who is the default user within the container?

  • Type whoami. This will give you root.

Exercises

3.3 Create a temporary file file1.txt in the current directory in the container. On your host, check the file permissions. Quit the interactive session.

  • Type touch file1.txt.

  • On Mac OS, this will give you on the and group staff.

  • On Linux, this will give you a file with root:root permissions.

Exercises

3.4 On the host, create a temporary file file2.txt in the current directory. Create a docker container and approach it interactively. In addition, mount your current directory to /data within the Docker container quay.io/biocontainers/fastqc:0.11.9--0. Check the file permissions of this file in the container.

  • Type touch file2.txt on the host.

  • In the container, this will give you on e.g. 1004:1004.
    The file will appear to have user ID (UID) and group ID (GID) numbers from the user that created this in the host. If these UID and GID do exist in the container, they may have a name instead.

Exercises

3.5 On the host, find out which UID and GID you have.

Hint

You can find your UID and GID with:

id -u
id -g

  • Running id -u will give you the effective user number, and id -g of the effective group number.

Exercises

3.6 Execute a docker container by using the -u option and in the meantime creating a temporary file file3.txt with touch. In addition, mount your current directory to /data within the Docker container quay.io/biocontainers/fastqc:0.11.9--0 Check the file permissions of this file in the container.

  • By using this command line, enter your UID and GID docker run --rm -u <your UID>:<your GID> quay.io/biocontainers/fastqc:0.11.9--0 touch file3.txt

  • Especially, on your Linux host, verify the file permissions of the file file3.txt.

4. Using working directories

Exercises

4.1 Execute a docker container by using the working directory option -w for a directory /workdir and creating a temporary file file4.txt with touch. In addition, mount your current directory to /workdir within the Docker container quay.io/biocontainers/fastqc:0.11.9--0. Check the file location of this file in the container.

  • docker run --rm -v $(pwd):/workdir -w /workdir -u 1000:1000 quay.io/biocontainers/fastqc:0.11.9--0 touch file4.txt

Exercises

4.2 Use the command docker inspect on the current image quay.io/biocontainers/fastqc:0.11.9--0 and extract the working directory (WorkingDir) using grep.

  • docker inspect quay.io/biocontainers/fastqc:0.11.9--0 | grep 'WorkingDir'

Exercises

4.3 Execute a docker container with your user and group ID running fastqc on the file WTXXX.fq.gz. In addition, mount your current directory to the default working directory within the Docker container quay.io/biocontainers/fastqc:0.11.9--0. Verify that the HTML report is created with the correct file permissions.

# Solution
docker run \
--rm \
-u "$(id -u):$(id -g)" \
-w /data
-v $(pwd)/data/:/data
quay.io/biocontainers/fastqc:0.11.9--0 \
fastqc WT1.fq.gz

Or instead of -v/--volume, use --mount:

--mount type=bind,source=$(pwd)/data/,target=/data \

Exercises

4.4 Go to Biocontainers.pro and find the Docker image of trimmomatic. In addition, mount your current directory to the default working directory within the Docker container of trimmomatic. Verify that the HTML report is created with the correct file permissions.

For this you can use the following set of parameters:

SE \
-threads 1 \
-phred33 \
input.fastq \
output.fastq \
ILLUMINACLIP:$ADAPTERS:2:30:10 \
SLIDINGWINDOW:4:5 \
LEADING:5 \
TRAILING:5 \
MINLEN:25

# Solution
docker run \
--rm \
-u="$(id -u):$(id -g)" \
--mount type=bind,source=$(pwd)/data/,target=/data \
quay.io/biocontainers/trimmomatic:XXXXX \
trimmomatic \
SE \
-threads 1 \
-phred33 \
input.fastq \
output.fastq \
ILLUMINACLIP:$ADAPTERS:2:30:10 \
SLIDINGWINDOW:4:5 \
LEADING:5 \
TRAILING:5 \
MINLEN:25

With the example data from this exercise, this results in the following command:

docker run \
--rm \
-u="$(id -u):$(id -g)" \
--mount type=bind,source=$(pwd)/data/,target=/data \
quay.io/biocontainers/trimmomatic:0.35--6 \
trimmomatic \
SE \
-threads 1 \
-phred33 \
data/ecoli_1.fastq.gz \
data/ecoli_1_trimmed.fastq.gz  \
ILLUMINACLIP:$ADAPTERS:2:30:10 \
SLIDINGWINDOW:4:5 \
LEADING:5 \
TRAILING:5 \
MINLEN:25