Run and execute Singularity images
Building Singularity images
Introduction to Singularity
part of material is based on: https://carpentries-incubator.github.io/singularity-introduction
More advanced image building
Different ways to build images. Know your base system and their packages. Popular ones: Debian CentOS Alpine Conda. Anaconda, Conda-forge, Bioconda, etc.
Building cache
Every line of a Dockerfile is actually an image/layer by itself. Modify for instance the last bit of the previous image (let’s change the image URL) and rebuild it (even with a different name/tag): It will start from the last line. This is OK most of the times and very convenient for testing and trying […]
tagging the images
To tag a local image with ID “e23aaea5dff1” into the “ubuntu_wget” image name repository with version “1.0”:
Starting the build
Implicitely looks for a Dockerfile file in the current directory: Syntax: –file / -f . stands for the context (in this case, current directory) of the build process. This makes sense if copying files from filesystem, for instance. IMPORTANT: Avoid contexts (directories) overpopulated with files (even if not actually used in the recipe). You can […]
More instructions for the recipes
Who is maintaining the container? WORKDIR: all subsequent actions will be executed in that working directory. ADD, COPY: add files to the image filesystem Difference between ADD and COPY explained here and here COPY: lets you copy a local file or directory from your host (the machine from which you are building the image) ADD: […]
Docker recipes: build your own images
Using existing images
Introduction to Docker
Thanks a lot for the excellent training content about Docker Biocore from CRG: https://github.com/biocorecrg/ELIXIR_containers_nextflowand Melbourne Bioinformatics https://www.melbournebioinformatics.org.au/tutorials/tutorials/docker/
Reading and writing files
Slides for this lesson Demo script for this lesson
Counting reads
DGE versus DTU
RNASeq workflow
Seurat: cluster and visualize cells
Write your own function
Statistical analyses
Slides for this lessonR script for this lesson
Make graphs with ggplot2
Conditional statements
Slides for this lesson
