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.