Merge pull request #26 from GitHubSecurityLab/sylwia-budzynska-patch-1

Enhance README with Docker and env variable instructions

Author: sylwia-budzynska

README.md

@@ -1,6 +1,12 @@
 ## SecLab taskflows
 
-This repository contains example taskflows to use with the [SecLab Taskflow Agent](https://github.com/GitHubSecurityLab/seclab-taskflow-agent), as well as the custom MCP servers that are needed to run the taskflows. To run these taskflows, first create a directory named `data` in `src`. Various environment variables need to be set for the custom MCP servers to store data.
+This repository contains example taskflows to use with the [SecLab Taskflow Agent](https://github.com/GitHubSecurityLab/seclab-taskflow-agent), as well as the custom MCP servers that are needed to run the taskflows. 
+
+### Running with docker script 
+
+The recommended way of running the taskflows in this repo is by creating a codespace, and running the script [`run_seclab_agent.sh`](https://github.com/GitHubSecurityLab/seclab-taskflows/blob/main/src/run_seclab_agent.sh) to run a docker container of the `seclab-taskflow-agent` as outlined [here](https://github.com/GitHubSecurityLab/seclab-taskflow-agent/tree/main?tab=readme-ov-file#deploying-from-docker). Note that this script needs to be run from the `src` directory, and the `.env` file with the environment variables for the custom MCP servers to store data needs to be in the same directory. 
+
+First, create a directory named `data` and a `.env` file in the `src` directory. For [`run_seclab_agent.sh`](https://github.com/GitHubSecurityLab/seclab-taskflows/blob/main/src/run_seclab_agent.sh) you can use:
 
 ```
 MEMCACHE_STATE_DIR=/app/data
@@ -9,22 +15,26 @@ DATA_DIR=/app/data
 LOG_DIR=/app/logs
 ```
 
-The `MEMCACHE_STATE_DIR` is needed to persist some intermediate data in the memcache, `DATA_DIR` is needed for various mcp servers to store intermediate results, and `LOG_DIR` is used to store log files generated by the servers. These can be set in a `.env` file in the `src` directory.
 
-If no environment variables are set for the custom MCP servers, relevant folders will be created automatically. The location depends on the platform, and is set by [`platformdirs`](https://pypi.org/project/platformdirs/).
+The `MEMCACHE_STATE_DIR` is needed to persist some intermediate data in the memcache, `DATA_DIR` is needed for various mcp servers to store intermediate results, and `LOG_DIR` is used to store log files generated by the servers. These can be set in a `.env` file in the `src` directory. If no environment variables are set for the custom MCP servers, relevant folders will be created automatically. The location depends on the platform, and is set by [`platformdirs`](https://pypi.org/project/platformdirs/).
 
-In addition, AI API endpoints and secrets also needs to be configured via [environment variables or Codespace secrets](https://github.com/GitHubSecurityLab/seclab-taskflow-agent?tab=readme-ov-file#configuration). In particular, the environment variables `AI_API_TOKEN` and `AI_API_ENDPOINT` needs to be set to the approach AI API endpoints and credentials. If not set, the default `AI_API_ENDPOINT` is GitHub models:
+In addition, AI API endpoints and secrets also need to be configured via [environment variables or Codespace secrets](https://github.com/GitHubSecurityLab/seclab-taskflow-agent?tab=readme-ov-file#configuration). In particular, the environment variables `AI_API_TOKEN` and `AI_API_ENDPOINT` need to be set to the appropriate AI API endpoints and credentials. If not set, the default `AI_API_ENDPOINT` is GitHub models:
 
 ```
 AI_API_ENDPOINT="https://models.github.ai/inference"
 ```
 
 In addition, the `GH_TOKEN` environment variable also needs to be set to allow interaction with the GitHub API, such as fetching content, creating issues etc.
 
-The repo provides a script [`run_seclab_agent.sh`](https://github.com/GitHubSecurityLab/seclab-taskflows/blob/main/src/run_seclab_agent.sh) to run a docker container of the `seclab-taskflow-agent` as outlined [here](https://github.com/GitHubSecurityLab/seclab-taskflow-agent/tree/main?tab=readme-ov-file#deploying-from-docker). Note that this script needs to be run from the `src` directory, and the `.env` file with the environmental variables needs to be in the same directory.
-
 Individual taskflows may need additional setup, please refer to the `README.md` in the relevant subdirectories for further requirements.
 
+After setting the relevant env vars, run an example taskflow with:
+
+```bash
+cd src
+./run_seclab_agent.sh -t seclab_taskflows.taskflows.audit.ghsa_variant_analysis_demo -g repo=github/cmark-gfm -g ghsa=GHSA-c944-cv5f-hpvr
+```
+
 ## Background
 
 [SecLab Taskflows](https://github.com/GitHubSecurityLab/seclab-taskflows) is a companion repository to the [SecLab Taskflow Agent](https://github.com/GitHubSecurityLab/seclab-taskflow-agent) repository.