pb-cdunn / falcon-examples

Examples on branches, and a useful place for testing

FALCON-examples

Examples, with test-cases, and a useful place for testing

To run, first build FALCON and its dependencies, and set-up your environment. (See FALCON-integrate in GitHub.) Then:

make run-ecoli

We do not recommend piping the output, since if you need to stop early (with Ctrl-C aka KeyboardInterrupt), your program might be killed before it has time to qdel the outstanding jobs.

Environment

One way to set-up your environment is to use Python virtualenv. Before running these examples, activate your virtualenv in your shell or via FALCON-integrate.

Data

*.fofn

These are "files of filenames". Since they are in the repo, they should be relative paths. (Relative to the current directory when they are used. But that is wrong. It should be relative to their own location. TODO)

Files

The repo source is lightweight because it contains symlinks instead of the contents of large files. These are managed by git-sym.

git-sym

This separates big-file caching from revision-control. There are several alternatives:

data directories

Relying on git-sym, symlinks to the data are stored in data/ sub-directories. The files should point (relatively) into .git_sym/, which contains more symlinks to a cache directory. git_sym.makefile should include a rule to produce files for those symlinks.