move stuff + readme.md

Dockerfile → tools/census-builder-workflow/Dockerfile

@@ -7,8 +7,8 @@ ENV COMMIT_SHA=${COMMIT_SHA}
 
 RUN apt update && apt -y install python3.10-venv python3-pip awscli
 
-ADD tools/cell_census_builder/ /tools/cell_census_builder
-ADD tools/scripts/requirements.txt .
+ADD cell_census_builder/ /tools/cell_census_builder
+ADD scripts/requirements.txt .
 ADD entrypoint.py .
 ADD build-census.yaml .
 

tools/census-builder-workflow/README.md

@@ -0,0 +1,45 @@
+# Cell Census Builder Workflow
+
+This subproject can be used to run a cell-census build using a Docker container and a custom workflow file.
+
+## Instructions
+
+### Build
+
+To build the docker container, `cd` into the parent folder (`tools/`) and run:
+
+```docker build --build-arg=COMMIT_SHA=$(git rev-parse --short HEAD) . -t census-builder```
+
+This will build a Docker container named `census-builder`.
+
+### Prepare
+
+Before running the workflow, make sure that a `data` directory exists on the machine. This can contain any inputs for the builder (e.g. a manifest file and local `h5ad`s), and will also be used to output the built cell census. This folder will also need to contain a `build-census.yaml` file as defined in the next step.
+
+
+### Create workflow file
+
+In the `data` folder, create a `build-census.yaml` file that contain a workflow that will be executed by the builder. This should also contain all the parameters for the workflow.
+
+Here is an example workflow that runs the builder using a manifest file:
+
+```
+census-builder:
+  uri:
+    /data/cell-census-small/
+  verbose:
+    true
+  commands:
+    build:
+      manifest:
+        /data/manifest-small.csv
+      test-disable-dirty-git-check:
+        true
+```
+
+
+### Run
+
+Run the builder workflow with:
+
+```docker run --mount type=bind,source="path/to/data",target=/data census-builder```

tools/census-builder-workflow/entrypoint.py

@@ -0,0 +1,3 @@
+#!/bin/python3
+
+print("Calling the builder...")