Dev.md

OSX Local Dev Notes

Requirements for Unittests

• sbt 0.13.16 (brew install sbt@0.13)
• oracle jdk 8 (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
• Postgres 9.6.x (https://postgresapp.com/documentation/all-versions.html)

Setup

DB Setup

Explicitly set PGDATA and PGPORT in .bashrc or .bash_profile. Also add path to psql to PATH

export PGPORT=5432
export PGDATA='/Users/mkocher/Library/Application Support/Postgres/var-9.6'
export PATH="/Applications/Postgres.app/Contents/Versions/9.6/bin:$PATH"

make db-reset-test
make db-reset-prod

Running/Compiling

sbt compile

Compile tests

sbt test:compile

Reformatting will happen on compilation.

Requirements Integration tests

• Python 2.7.13 using Conda or MiniConda (https://conda.io/miniconda.html)
• Subset of PacBio python repos (defined below)

Create Conda Env

Create an Env named smrtflow

conda create --name smrtflow requests cython numpy matplotlib jupyter

Activate python env in the current shell

source activate smrtflow

Install pysam and ngmlr

conda install -c bioconda pysam ngmlr

Better Postgres CLI tool

pip install pgcli

Pull the following PacBio repos

(using the standard $USER env var)

git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/chemistry-data-bundle.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/pbcommand.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/pbpipeline-resources.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/pbreports.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/pbsmrtpipe.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/pysiv2.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/siv-tests.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/smrtflow.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sl/testkit-jobs.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sat/pbcore.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sat/pbcoretools.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sat/pacbiotestdata.git
git clone http://$USER@bitbucket.nanofluidics.com:7990/scm/sat/pacbiotestdata.git

cd pbcore && pip install . && cd -
cd pbcommand && pip install . && cd -
cd pbsmrtpipe && pip install . && cd -
cd pbcoretools && pip install . && cd -
cd pbreports && pip install  . && cd -

Running Integration tests

Source the conda env, the run the make target

source activate smrtflow
make test-int