diff --git a/README.md b/README.md index 81f3829..3a5701f 100644 --- a/README.md +++ b/README.md @@ -5,12 +5,12 @@ ___cwl-tes___ submits your tasks to a TES server. Task submission is parallelized when possible. -[Funnel](https://ohsu-comp-bio.github.io/funnel) is an implementation of the [GA4GH task execution API](https://github.com/ga4gh/task-execution-schemas). It runs your dockerized tasks on slurm, htcondor, google compute engine, etc. +[Funnel](https://ohsu-comp-bio.github.io/funnel) is an implementation of the [GA4GH task execution API](https://github.com/ga4gh/task-execution-schemas). It runs your dockerized tasks on slurm, htcondor, google compute engine, aws batch, etc. ## Requirements -* Python 2.7 +* Python 2.7 / 3.5 / 3.6 * [Docker](https://docs.docker.com/) @@ -21,7 +21,7 @@ ___cwl-tes___ submits your tasks to a TES server. Task submission is parallelize * Start the task server ``` -funnel server +funnel server run ``` * Run your CWL tool/workflow @@ -32,7 +32,17 @@ cwl-tes --tes http://localhost:8000 tests/hashsplitter-workflow.cwl.yml --input ## Install -To install from source: +I strongly reccommend using a [virutalenv](https://virtualenv.pypa.io/en/stable/#) for installation since _cwl-tes_ +depends on a specific version of _cwltool_. + +Install from pip: + +``` +pip install cwl-tes +``` + + +Install from source: ``` python setup.py install @@ -44,7 +54,7 @@ python setup.py install To start a funnel server instance automatically and run all of the conformance tests: ``` -nosetests -w ./tests +python -m nose ./tests ``` @@ -58,8 +68,14 @@ funnel server --config /path/to/config.yaml Make sure that TMPDIR is specified in the AllowedDirs of your Local storage configuration. -Run the tests. +To run all the tests: ``` ./tests/run_conformance.sh ``` + +To run a specifc test: + +``` +./tests/run_conformance.sh 10 +```