Testing flair

Prerequisites:

  • You have all of the FLAIR dependencies install, normally through conda

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

Move to the flair/test directory, then run make test or run tests in parallel with make -O -j 32 test.

By default, this uses the FLAIR code in the tree, to teat install FLAIR, use make test use_installed_flair=yes.

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 four 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-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 unless you specific the -k option 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.