Updating - PacificBiosciences/FALCON-integrate GitHub Wiki

See Installation for more explanation.

Using a "standard" Python installation

rm -rf fc_env virtualenv  # necessary if you are upgrading from an older git revision
git checkout 0.4.0  # or whatever version you want
make init
source env.sh
make config-standard
make -j install
make test  # to run a simple one

note: do not run make clean after building, as binaries are symlinked to the bin directory, not copied.

Using an "editable" installation

If you are using a fairly recent version, it's all so much simpler! Hopefully, you used make config-edit or make config-edit-user when you installed. Then, to update:

git pull origin master  # or whatever version you want
git submodule update
make -j install
make test  # to run a simple one

In fact, if only pure Python code changes, you don't even need to re-run make install.