Setup: Installation and Environment

Detailed steps for installation

We strongly recommend that you try our integration modules:

• FALCON-make for building
• FALCON-examples for testing
• FALCON-integrate for consistent git-submodule revisions
  • https://github.com/PacificBiosciences/FALCON-integrate
  • https://github.com/PacificBiosciences/FALCON-integrate/wiki

However, if you want to use your own system for building or testing, read on.

Linux environment

Here is the environment used in this example, to construct a user-space python virtualenv for running Falcon.

uname -a
## Linux login14-biofx 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 GNU/Linux

gcc --version
## gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
## Copyright (C) 2013 Free Software Foundation, Inc.
## This is free software; see the source for copying conditions.  There is NO
## warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

# We also use GNU make, which might be called 'make' or 'gmake'.

python --version
## Python 2.7.6

# We do plan to move to Python 3 sometime.

Python virtualenv

We install everything as a Python virtualenv in a shared directory across the computational nodes:

FC=$(pwd)/fc_env
virtualenv --no-site-packages  --always-copy   $FC
## New python executable in /home/UNIXHOME/jchin/task2014/falcon_pb_github/fc_env/bin/python
## Installing setuptools, pip, wheel...done.

# Activate the virtual environment.
. $FC/bin/activate
which python
## $FC/bin/python

Git submodules

We will need two python packges, pypeFLOW and FALCON, and we need to compile the DALINGER and DAZZ_DB code and put the binary executables into the virtual environment.

These are all git submodules of FALCON-integrate.

git clone git://github.com/PacificBiosciences/FALCON-integrate.git
cd FALCON-integrate

# Fetch submodules.
git submodule update --init

## Submodule 'DALIGNER' (git://github.com/pb-jchin/DALIGNER.git) registered for path 'DALIGNER'
## Submodule 'DAZZ_DB' (git://github.com/pb-jchin/DAZZ_DB.git) registered for path 'DAZZ_DB'
## Submodule 'FALCON' (git://github.com/PacificBiosciences/FALCON.git) registered for path 'FALCON'
## Submodule 'pypeFLOW' (git://github.com/PacificBiosciences/pypeFLOW.git) registered for path 'pypeFLOW'

Building and installing

# Install dependencies.

cd pypeFLOW
python setup.py install
cd ..

cd FALCON
python setup.py install
cd ..

cd DAZZ_DB/
make
cp DBrm DBshow DBsplit DBstats fasta2DB $FC/bin/
cd ..

cd DALIGNER
make
cp daligner daligner_p DB2Falcon HPCdaligner LA4Falcon LAmerge LAsort  $FC/bin
cd ..