Installing 0.7.3 and using on SLURM

[JohnUrban]

Hi,

We recently chatted a lot ( #50 and #53 ) about getting 0.6.2 to work on SLURM, which in part led to 0.6.3.

Since I am starting assemblies now, I might as well update to the latest, which I believe is 0.7.3.

The old way of installing that was successful for 0.6.2 no longer works:

#!/bin/bash
module load git
git clone git://github.com/PacificBiosciences/FALCON-integrate.git
cd FALCON-integrate
git checkout 0.6.2
make init
make virtualenv
make check
unset PYTHONPATH
make -j install
make test  # to run a simple one

So I followed the newer instructions you have (https://github.com/PacificBiosciences/FALCON-integrate/wiki/Installation, 'the easy way'), but I had to use "unset PYTHONPATH" again for it to install and run the make tests successfully :

#!/bin/bash
module load git
git clone git://github.com/PacificBiosciences/FALCON-integrate.git
cd FALCON-integrate
git checkout 0.7.3 # or master or whatever version you want
unset PYTHONPATH
make init
source env.sh
make config-edit-user
make -j all
make test  # to run a simple one

As far as getting through the installation and make tests, it seems to have worked after adding unset PYTHONPATH.

The next thing to do is to run it on synth0 to make sure.
The way I used to run it with 0.6.2 was (slurm batch script):

#!/bin/bash
#SBATCH -J falcon-synth0-1
#SBATCH -c 4
#SBATCH --qos=biomed-sb-condo
#SBATCH --mem=4g
#SBATCH --time=00:30:00
###########################
unset PYTHONPATH
. ~/software/falcon62/FALCON-integrate/fc_env/bin/activate
fc_run.py fc_run.cfg logging.ini

However, FALCON-integrate/fc_env/bin/activate seems to be missing.
How do you suggest I run it? Do I need to activate a virtualenv? Can I just put FALCON-integrate/fc_env/bin in the PATH?

Thanks as usual.

[pb-cdunn]

• PYTHONPATH can cause problems for virtualenv too. If you already have falcon or dependencies installed somewhere that is available via PYTHONPATH, then yes, you might need to unset it.
• fc_env/bin/activate was for virtualenv. You can continue to use virtualenv if you want. We no longer ship it with FALCON-integrate because it does not work on all systems, but it seems to work on your. Simply change the one line in the installation instructions: make config-edit instead of make config-edit-user. A "user" install relies on your PYTHONUSERBASE. (Google it.) It is even more sensitive to your PYTHONPATH than virtualenv would be.
• Yes, you need FALCON-integrate/fc_env/bin in your PATH. It will already be there if you source env.sh.