Update README.md

README.md

@@ -1,5 +1,5 @@
 # Galaxy Benchmarker
-A tool for benchmarking Galaxy job-destinations. 
+A tool for benchmarking Galaxy job-destinations.
 
 The goal is to easily benchmark different job-destinations. All you have to do is to configure the benchmarker itself,
 define the destinations you want to benchmark, the workflows you want to run and the benchmarks you want to use. GalaxyBenchmarker
@@ -15,7 +15,7 @@ be run per destination and if some ansible-playbooks should be run before or aft
 What is the difference between running a workflow for the first time or for it having been run multiple
 times already? What is the overhead for staging time, installing tools, etc?
 
-This benchmark cleans up Pulsar for every cold run, using a Ansible-Playbook ([coldwarm_pretask.yml]). 
+This benchmark cleans up Pulsar for every cold run, using a Ansible-Playbook ([coldwarm_pretask.yml]).
 
 #### Destination Comparison
 What are the differences between multiple destinations in terms of staging time (sending data
@@ -33,9 +33,77 @@ How does a destination handle a big burst of requests?
 * Ansible
 
 ## Usage
-* Configure the benchmarker. Examples can be found in [benchmark_config.yml.example].
-* Run 
+### Install all dependencies
+Some additional packages are needed in order for GalaxyBenchmarker to function properly. 
+To install those, run the following command:
+```shell
+pip3 install -r requirements.txt
+```
 
-        python galaxy_benchmarker
-
-* Analyze metrics in InfluxDB. Example Dashboards for Grafana can be found at [./grafana_dashboards] 
+### Configure the GalaxyBenchmarker
+To use the benchmarker, you first need to create a yaml-configuration file.
+We need to have access to a Galaxy instance in order to submit workflows:
+```yaml
+galaxy:
+  url: https://usegalaxy.eu
+  user_key: YOUR-KEY
+```
+
+Next, we need to define the workflows that should be run. The benchmarker
+uses the test functionality of [Planemo](https://github.com/galaxyproject/planemo) to 
+submit workflows. Examples can be found at: https://github.com/usegalaxy-eu/workflow-testing. For a start, you
+can clone this repository and use those workflows for benchmarking. Workflows are defined in the
+configuration as following:
+```yaml
+workflows:
+  - name: ARDWorkflow
+    type: Galaxy
+    path: /../workflow-testing/sklearn/ard/ard.ga
+```
+
+The benchmarker can submit jobs to multiple job destinations to compare the performance of each. For routing
+the jobs to the right destination, users can be defined for each. The GalaxyBenchmarker can take 
+care of that 
+(see the [configuration examples](https://github.com/AndreasSko/Galaxy-Benchmarker/blob/master/benchmark_config.yml.example)) 
+if you are an administrator for the Galaxy instance. Otherwise, it is also possible to use different
+users for each destination and link them in the configuration of the benchmarker:
+```yaml
+destinations:
+  - name: Destination1
+    type: Galaxy
+    galaxy_user_name: USERNAME
+    galaxy_user_key: USERKEY
+```
+
+Now, we just need to define the actual benchmark that we want to perform. To compare different job destinations, 
+you can do the following:
+```yaml
+benchmarks:
+  - name: DestinationComparisonBenchmark
+    type: DestinationComparison
+    destinations:
+      - Destination1
+    workflows:
+      - ARDWorkflow
+    runs_per_workflow: 1
+```
+
+### Run the benchmarks
+The GalaxyBenchmarker can use different configuration files. If none is given, it will look for `benchmark_config.yml`
+```shell
+python3 galaxy_benchmarker --config benchmark_config.yml
+```
+
+## Additional options
+### InfluxDB
+In normal cases, GalaxyBenchmarker will save the results in a json file under the `results` directory. However, jobs 
+metrics can also be submitted to InfluxDB for further analysis.
+```yaml
+influxdb:
+  host: influxdb.example.com
+  port: 8086
+  username: glx_benchmarker_user
+  password: supersecret
+  db_name: glx_benchmarker
+```
+Example Dashboards for Grafana can be found at [grafana_dashboards](https://github.com/AndreasSko/Galaxy-Benchmarker/tree/master/grafana_dashboards)