- sbt 0.13.16 (
brew install [email protected]) - 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)
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
sbt compile
Compile tests
sbt test:compile
Reformatting will happen on compilation.
- Python 2.7.13 using
CondaorMiniConda(https://conda.io/miniconda.html) - Subset of PacBio python repos (defined below)
Create an Env named smrtflow
conda create --name smrtflow requests cython numpy matplotlib jupyter
Activate python env in the current shell
source activate smrtflow
conda install -c bioconda pysam ngmlr
pip install pgcli
Pull the following PacBio repos
(using the standard $USER env var)
git clone http://[email protected]:7990/scm/sl/chemistry-data-bundle.git
git clone http://[email protected]:7990/scm/sl/pbcommand.git
git clone http://[email protected]:7990/scm/sl/pbpipeline-resources.git
git clone http://[email protected]:7990/scm/sl/pbreports.git
git clone http://[email protected]:7990/scm/sl/pbsmrtpipe.git
git clone http://[email protected]:7990/scm/sl/pysiv2.git
git clone http://[email protected]:7990/scm/sl/siv-tests.git
git clone http://[email protected]:7990/scm/sl/smrtflow.git
git clone http://[email protected]:7990/scm/sl/testkit-jobs.git
git clone http://[email protected]:7990/scm/sat/pbcore.git
git clone http://[email protected]:7990/scm/sat/pbcoretools.git
git clone http://[email protected]:7990/scm/sat/pacbiotestdata.git
git clone http://[email protected]: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 -
Source the conda env, the run the make target
source activate smrtflow
make test-int