Tapis Workflow Installation and ExecutionΒΆ

Install GeneFlow and Tapis dependencies into a Python virtual environment:

# create a virtual python environment
mkdir -p ~/geneflow
cd ~/geneflow
python -m venv gfpy
source gfpy/bin/activate

# install geneflow
pip3 install geneflow

# install tapis/agave library
git clone -b python-3.7 https://gitlab.com/geneflow/dependencies/agavepy.git
pip3 install ./agavepy

Create an Tapis/Agave token. There are a couple ways to do this, but in the CDC environment, the recommended method is the cobra-cli module:

module load cobra-cli
auth-tokens-create -u [username]

Create a personal execution system. This is required to be able to register apps to the system:


Create the GeneFlow config file with the following contents:

vim ./config.yaml
class: config
gfVersion: v2.0
    connection_type: agave-cli
    path: database.db
    type: sqlite

Create the GeneFlow agave-params file with the following contents. Replace [username] with your username and replace [date] with the date associated with your personal execution system.

vim ./agave-params.yaml
%YAML 1.1
  # prefix for app name. For user apps, use your username.
  # For public apps, use 'public'.
  appsPrefix: [username]

  # must have publish rights to the execution system
  executionSystem: cobra-hpc-aspen-[username]-[date]

  # location of your agave home directory
  deploymentSystem: tapis-default-public-storage

  # Apps directory where app assets will be uploaded.
  # This must be an absolute path.
  appsDir: /[username]/apps-gf

  # location of workflow test data, absolute path.
  testDataDir: /[username]/testdata-gf

Install the workflow and register with Agave:

gf install-workflow -g https://gitlab.com/workflows/bwa-gf2.git -c --make-apps --config ./config.yaml -e local --agave-params ./agave-params.yaml bwa-gf2

Run the workflow, replace [username] with your username:

gf --log-level debug run ./bwa-gf2 -o ./output -n test-agave -w agave://tapis-default-public-storage/[username]/.geneflow/work --in.files ./bwa-gf2/data/reads --in.reference ./bwa-gf2/data/reference/poliovirus_strain_Sabin1.fasta --ec default:agave --ep default.slots:2