Testing flair

Prerequisites:

  • flair and flair scripts are in your $PATH (see below)

  • You have a copy of the flair/test directory (e.g. git clone git@github.com:BrooksLabUCSC/flair.git)

  • GNU make

Flair is in your $PATH if you used conda install -c conda-forge -c bioconda flair.

If you downloaded the latest release from github or cloned the flair repository:

export PATH=/path/to/flair/src/flair:/path/to/flair/bin:$PATH

Move to the flair/test directory, then run make test.

If this is the first time, make will download some sequences from the UCSC Genome Browser download page and store them as test_input/genome.fa.

make test tests all six flair modules and two helper programs. You can also test them individually using:

  • make test-align

  • make test-correct

  • make test-collapse

  • make test-quantify

  • make test-diffexp

  • make test-diffsplice

  • make test-predict-productivity

  • make test-diff-iso-usage

make outputs a lot of information. If a test fails, it will stop with an error and not run any additional tests. Errors look like this:

make: *** [makefile:71: test-predict-productivity] Error 2

You can usually find more information in the lines preceding the error. If you cannot figure out the problem, please create a ticket.