Skip to content

README.md

Latest commit

 

History

History
61 lines (44 loc) · 2.52 KB

README.md

File metadata and controls

61 lines (44 loc) · 2.52 KB

Travis Build Status Docker Build Status

Gene-set analysis tutorial

User info:

GSA tutorial link: https://varemo.github.io/GSA_tutorial/functional_annotation.html

This tutorial will take roughly 3-6h depending on previous experience.

(Suggested answers to the questions are available on request)

Developer notes

Files

GSA_tutorial
|
|- data/                        # data file needed to carry out the tutorial
|- slides/                      # slides used for presentations
|
|- .travis.yml                  # Travis CI settings (see info below)
|- Dockerfile                   # Instructions to build a Docker image (see info below)
|- data.zip                     # compressed data/ directory with data needed for the tutorial
|- functional_annotation.Rmd    # Rmd file that is used to generate the html tutorial page (see info below)

GitHub

GitHub push -->

  • new Docker built automatically on Docker hub, available through docker pull
  • Travis CI testing and webpage deployment

Commits are tagged at each course for easy access of the state of the repo at a given course (see Releases).
Travis status badge added to README.md from Travis.

Dockerfile

  • Built from bioconductor/release_core2:R3.4.2_Bioc3.6 image that contains R and Rstudio.
  • Adds on:
    • installation of required R packages
    • data/ directory

In Docker Hub: Create Auto-build from GitHub was selected to get the automated build to work. This means that the image can be pulled (without building locally) by docker pull varemo/GSA_tutorial. At Docker hub one can set build settings. Here a build was set on relevant git tags (i.e. courses). So one can e.g. run docker pull varemo/GSA_tutorial:NGS_course_GU_2017 to get the Docker image in the state it was at that course.

Travis CI

Connect to GitHub repo at travis-ci.org. This sets up automatic testing at push to GitHub. A GitHub token is added as an Environmental variable under settings at travis-ci.org. The token is created in GitHub under user settings - Developer settings - Personal access tokens. The Travis CI testing includes:

  • test Docker build from Docker file
  • test run code in Rmd file
  • build html from Rmd file
  • make a copy of html file where answers are displayed
  • push back the 2 html files to gh-pages branch on GitHub