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Welcome to the FALCON-examples wiki!

Usage

# This assumes you have done the vanilla installation described in this wiki.
cd FALCON-integrate

# If you ran `make config-edit-user`, you need to set `PYTHONUSERBASE`, `PATH`, and `(DY)LD_LIBRARY_PATH` in your environment.
source env.sh

# Alternatively, if you did a "system install" into your own virtualenv,
# activate the Virtualenv which was created for you by `make virtualenv` in the
# `fc_env` subdirectory.
. fc_env/bin/activate

# Here are the examples. They are found in the `run` subdirectory.
cd FALCON-examples

# Note how the examples are configured regarding running on a cluster (sge) or 
# locally (local). If the job_type is not set, then the default is `sge`
grep job_type run/*/*.cfg

make run-synth0

# Or equivalently (you can run it twice, it won't hurt, as the Makefile will 
# prevent the commands from rerunning.
cd run/synth0
make

# Output will be in the 0-*, 1-* and 2-* directories.

# Let's go back up and try some more
cd ../..

# Here are some more challenging data sets. If the data is not present,
# then manually create symlinks
make run-ecoli
make run-arab
make run-ecoli2
make run-lambda
make run-lambda-hgap
make run-lambda-smb14

Note: Not all test-data are available publicly.

Explanation

We assume you have already set up a Python virtualenv. You should have run make virtualenv in the installation, or done you own virtualenv.

FALCON-examples contains a variety of test-cases, some of which are available publicly. It uses git-sym to retrieve (and cache) test-data, in order to keep the repository size small. You can use FALCON-examples as a template for your own testing.

The simple makefile (using gnu-make) matches patterns (run-%:) to setup and run the tests. Each test-case is under the run directory and follows a similar structure.

FALCON-integrate runs a test-case in FALCON-examples as part of our continuous integration suite.

Note: The job_type configuration value in the fc_run.cfg file determines if FALCON runs in sge (aka qsub cluster mode) or local (i.e. on the local machine). See the *.cfg file first to see how the example is configured.