diff --git a/.github/workflows/build-containers.yml b/.github/workflows/build-containers.yml
index 15f565650..2ced59786 100644
--- a/.github/workflows/build-containers.yml
+++ b/.github/workflows/build-containers.yml
@@ -12,57 +12,57 @@ jobs:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/OmicsIntegrator1
-      container: reedcompbio/omics-integrator-1
+      container: ghcr.io/reed-compbio/omics-integrator-1
   build-and-remove-omics2:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/OmicsIntegrator2
-      container: reedcompbio/omics-integrator-2
+      container: ghcr.io/reed-compbio/omics-integrator-2
   build-and-remove-pathlinker:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/PathLinker
-      container: reedcompbio/pathlinker
+      container: ghcr.io/reed-compbio/pathlinker
   build-and-remove-meo:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/MEO
-      container: reedcompbio/meo
+      container: ghcr.io/reed-compbio/meo
   build-and-remove-mincostflow:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/MinCostFlow
-      container: reedcompbio/mincostflow
+      container: ghcr.io/reed-compbio/mincostflow
   build-and-remove-allpairs:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/AllPairs
-      container: reedcompbio/allpairs
+      container: ghcr.io/reed-compbio/allpairs
   build-and-remove-domino:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/DOMINO
-      container: reedcompbio/domino
+      container: ghcr.io/reed-compbio/domino
   build-and-remove-btb:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/BowTieBuilder
-      container: reedcompbio/bowtiebuilder
+      container: ghcr.io/reed-compbio/bowtiebuilder
   build-and-remove-cytoscape:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/Cytoscape
-      container: reedcompbio/py4cytoscape
+      container: ghcr.io/reed-compbio/py4cytoscape
   build-and-remove-responsenet:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/ResponseNet
-      container: reedcompbio/responsenet
+      container: ghcr.io/reed-compbio/responsenet
   build-and-remove-spras:
     uses: "./.github/workflows/build-and-remove-template.yml"
     with:
       path: docker-wrappers/SPRAS
-      container: reedcompbio/spras
+      container: ghcr.io/reed-compbio/spras
       # Since any change to the SPRAS codebase would constitute a change to
       # the container we produce in this step, build the container regardless
       # of detected changes.
diff --git a/.github/workflows/push-docker.yml b/.github/workflows/push-docker.yml
new file mode 100644
index 000000000..43ea19944
--- /dev/null
+++ b/.github/workflows/push-docker.yml
@@ -0,0 +1,30 @@
+name: Push to Docker
+
+on:
+  workflow_dispatch:
+    inputs:
+      folder:
+        description: 'The folder to push'
+        required: true
+        type: string
+      version:
+        description: 'The version to use (e.g. v1)'
+        required: true
+        type: string
+
+jobs:
+  push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Run build.py
+        run: python3 docker-wrappers/build.py --dir ${{ inputs.folder }} --version ${{ inputs.version }} --yes
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index cf4ee6157..9d4369380 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -19,25 +19,12 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Log in to Docker Hub
+      - name: Login to GitHub Container Registry
         uses: docker/login-action@v3
         with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          # Passwords are set up through the GitHub control panel. The docs for
-          # the login action are explicit about never using a real password, and
-          # instead setting up a DockerHub personal access token:
-          # https://github.com/docker/login-action?tab=readme-ov-file#docker-hub
-          password: ${{ secrets.DOCKER_PASSWORD }}
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v6
-        with:
-          context: ./
-          file: docker-wrappers/SPRAS/Dockerfile
-          tags: |
-            reedcompbio/spras:${{ github.ref_name }}
-            reedcompbio/spras:latest
-          # Use the previous latest for the build cache, assuming they're probably
-          # relatively similar
-          cache-from: type=registry,ref=reedcompbio/spras:latest
-          push: true
+        run: python3 docker-wrappers/build.py --dir SPRAS --version ${{ github.ref_name }} --yes
diff --git a/README.md b/README.md
index 44895c76b..ed1f2fa01 100644
--- a/README.md
+++ b/README.md
@@ -72,7 +72,7 @@ Large SPRAS workflows may benefit from execution with HTCondor, a scheduler/mana
 **Dockerized pathway reconstruction algorithms**: Pathway reconstruction algorithms are run via Docker images using the docker-py Python package.
 [PathLinker](https://github.com/Murali-group/PathLinker), [Omics Integrator](https://github.com/fraenkel-lab/OmicsIntegrator), [Omics Integrator 2](https://github.com/fraenkel-lab/OmicsIntegrator2), and [Maximum Edge Orientation](https://github.com/agitter/meo/) are the first supported algorithms.
 The files to create these Docker images are in the `docker-wrappers` subdirectory along with links to algorithms' original repositories.
-The Docker images are available on [DockerHub](https://hub.docker.com/orgs/reedcompbio).
+The Docker images are available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages).
 
 **Python wrapper for calling algorithms**: Wrapper functions provide an interface between the common file formats for input and output data and the algorithm-specific file formats and reconstruction commands.
 These wrappers are in the `spras/` subdirectory.
diff --git a/config/config.yaml b/config/config.yaml
index f2899fb9a..75603e112 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -24,10 +24,10 @@ containers:
   # Note that this assumes container names are consistent across registries, and that the
   # registry being passed doesn't require authentication for pull actions
   registry:
-    base_url: docker.io
+    base_url: ghcr.io
     # The owner or project of the registry
-    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
-    owner: reedcompbio
+    # For example, "reed-compbio" if the image is available as ghcr.io/reed-compbio/allpairs
+    owner: reed-compbio
 
   # Enabling profiling adds a file called 'usage-profile.tsv' to the output directory of each algorithm.
   # The contents of this file describe the CPU utilization and peak memory consumption of the algorithm
diff --git a/config/egfr.yaml b/config/egfr.yaml
index b93c593c4..9cf873540 100644
--- a/config/egfr.yaml
+++ b/config/egfr.yaml
@@ -21,10 +21,10 @@ containers:
   # Note that this assumes container names are consistent across registries, and that the
   # registry being passed doesn't require authentication for pull actions
   registry:
-    base_url: docker.io
+    base_url: ghcr.io
     # The owner or project of the registry
-    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
-    owner: reedcompbio
+    # For example, "reed-compbio" if the image is available as ghcr.io/reed-compbio/allpairs
+    owner: reed-compbio
 
 algorithms:
   - name: pathlinker
diff --git a/docker-wrappers/AllPairs/Dockerfile b/docker-wrappers/AllPairs/Dockerfile
index 332915d17..738b56158 100644
--- a/docker-wrappers/AllPairs/Dockerfile
+++ b/docker-wrappers/AllPairs/Dockerfile
@@ -1,5 +1,6 @@
 # AllPairs wrapper
 FROM python:3.12-alpine3.21
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # bash is required for dsub in the All of Us cloud environment
 RUN apk add --no-cache bash
diff --git a/docker-wrappers/AllPairs/README.md b/docker-wrappers/AllPairs/README.md
index fb366c5a4..3110668f2 100644
--- a/docker-wrappers/AllPairs/README.md
+++ b/docker-wrappers/AllPairs/README.md
@@ -1,17 +1,17 @@
 # All Pairs Shortest Paths Docker image
 
-A Docker image for All Pairs Shortest Paths that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/allpairs).
+A Docker image for All Pairs Shortest Paths that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/allpairs).
 This [algorithm](https://github.com/Reed-CompBio/all-pairs-shortest-paths) was implemented by the SPRAS team and relies on the NetworkX [`shortest_path`](https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html) function.
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/allpairs -f Dockerfile .
+docker build -t reed-compbio/allpairs -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-docker run reedcompbio/allpairs pip list
+docker run reed-compbio/allpairs pip list
 ```
 
 
@@ -29,3 +29,4 @@ The Docker wrapper can be tested with `pytest -k test_ap.py` from the root of th
 ## Versions:
 - v1: Initial version. Copies source file from SPRAS repository.
 - v2: Add bash, which is not available in Alpine Linux.
+- v3: AllPairs directionality
diff --git a/docker-wrappers/AllPairs/metadata.json b/docker-wrappers/AllPairs/metadata.json
new file mode 100644
index 000000000..860ebdc5a
--- /dev/null
+++ b/docker-wrappers/AllPairs/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "allpairs",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/BowTieBuilder/Dockerfile b/docker-wrappers/BowTieBuilder/Dockerfile
index 750832c0d..1aa095a51 100644
--- a/docker-wrappers/BowTieBuilder/Dockerfile
+++ b/docker-wrappers/BowTieBuilder/Dockerfile
@@ -1,4 +1,5 @@
 FROM python:3.8-bullseye
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /btb
 RUN wget https://raw.githubusercontent.com/Reed-CompBio/BowTieBuilder-Algorithm/dd8519cd8a8397c0e0724106f498b6002d3f7be2/btb.py
diff --git a/docker-wrappers/BowTieBuilder/README.md b/docker-wrappers/BowTieBuilder/README.md
index d0b80ee76..ec92b44f5 100644
--- a/docker-wrappers/BowTieBuilder/README.md
+++ b/docker-wrappers/BowTieBuilder/README.md
@@ -1,10 +1,10 @@
 # BowTieBuilder Docker image
 
-A Docker image for [BowTieBuilder](https://github.com/Reed-CompBio/BowTieBuilder-Algorithm) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/bowtiebuilder).
+A Docker image for [BowTieBuilder](https://github.com/Reed-CompBio/BowTieBuilder-Algorithm) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/bowtiebuilder).
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/bowtiebuilder:v2 -f Dockerfile .
+docker build -t reed-compbio/bowtiebuilder:v1 -f Dockerfile .
 ```
 from this directory.
 
@@ -12,4 +12,9 @@ from this directory.
 
 The original paper for [BowTieBuilder] can be accessed here:
 
-Supper, J., Spangenberg, L., Planatscher, H. et al. BowTieBuilder: modeling signal transduction pathways. BMC Syst Biol 3, 67 (2009). https://doi.org/10.1186/1752-0509-3-67
\ No newline at end of file
+Supper, J., Spangenberg, L., Planatscher, H. et al. BowTieBuilder: modeling signal transduction pathways. BMC Syst Biol 3, 67 (2009). https://doi.org/10.1186/1752-0509-3-67
+
+## Versions
+
+- `v1`: Initial docker container
+- `v2`: Pin BTB file version for reproducible docker builds.
diff --git a/docker-wrappers/BowTieBuilder/metadata.json b/docker-wrappers/BowTieBuilder/metadata.json
new file mode 100644
index 000000000..9643780e2
--- /dev/null
+++ b/docker-wrappers/BowTieBuilder/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "bowtiebuilder",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/Cytoscape/Dockerfile b/docker-wrappers/Cytoscape/Dockerfile
index 308373474..e7a665cdf 100644
--- a/docker-wrappers/Cytoscape/Dockerfile
+++ b/docker-wrappers/Cytoscape/Dockerfile
@@ -2,6 +2,7 @@
 # https://github.com/cytoscape/docker-cytoscape-desktop/blob/173ab46b4b5e5c148113ad0c9960a6af3fc50432/py4cytoscape/Dockerfile
 # by Kozo Nishida
 FROM python:3.9.13
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # Versions
 ENV CYTOSCAPE_VERSION=3.9.1
diff --git a/docker-wrappers/Cytoscape/README.md b/docker-wrappers/Cytoscape/README.md
index c3cb89672..e54fe7f99 100644
--- a/docker-wrappers/Cytoscape/README.md
+++ b/docker-wrappers/Cytoscape/README.md
@@ -1,6 +1,6 @@
 # Cytoscape image
 
-A Docker image for [Cytoscape](https://cytoscape.org/) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/py4cytoscape).
+A Docker image for [Cytoscape](https://cytoscape.org/) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/py4cytoscape).
 It was originally derived from the [`docker-cytoscape-desktop/py4cytoscape`](https://github.com/cytoscape/docker-cytoscape-desktop/blob/173ab46b4b5e5c148113ad0c9960a6af3fc50432/py4cytoscape/Dockerfile) image.
 
 Thank you to Scooter Morris for help debugging problems running Cytoscape in Singularity.
@@ -9,7 +9,7 @@ Thank you to Scooter Morris for help debugging problems running Cytoscape in Sin
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/py4cytoscape -f Dockerfile .
+docker build -t reed-compbio/py4cytoscape -f Dockerfile .
 ```
 from this directory.
 
diff --git a/docker-wrappers/Cytoscape/metadata.json b/docker-wrappers/Cytoscape/metadata.json
new file mode 100644
index 000000000..908245564
--- /dev/null
+++ b/docker-wrappers/Cytoscape/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "py4cytoscape",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/DOMINO/Dockerfile b/docker-wrappers/DOMINO/Dockerfile
index 9ab193ac4..75e905c37 100644
--- a/docker-wrappers/DOMINO/Dockerfile
+++ b/docker-wrappers/DOMINO/Dockerfile
@@ -1,6 +1,7 @@
 # DOMINO wrapper
 # https://github.com/Shamir-Lab/DOMINO
 FROM python:3.7
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 RUN pip install domino-python==0.1.1
 
diff --git a/docker-wrappers/DOMINO/README.md b/docker-wrappers/DOMINO/README.md
index 610c73bc8..3aa37e9b5 100644
--- a/docker-wrappers/DOMINO/README.md
+++ b/docker-wrappers/DOMINO/README.md
@@ -1,22 +1,27 @@
 # DOMINO Docker image
 
-A Docker image for [DOMINO](https://github.com/Shamir-Lab/DOMINO) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/domino).
+A Docker image for [DOMINO](https://github.com/Shamir-Lab/DOMINO) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/domino).
 
 DOMINO outputs multiple active modules, which SPRAS combines into a single pathway.
 It is [non-deterministic](https://github.com/Shamir-Lab/DOMINO/issues/5) and cannot be made deterministic with a seed.
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/domino -f Dockerfile .
+docker build -t reed-compbio/domino -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-winpty docker run reedcompbio/domino pip list
+winpty docker run reed-compbio/domino pip list
 ```
 The `winpty` prefix is only needed on Windows.
 
 ## TODO
 - Resolve upstream ValueError with small inputs https://github.com/Shamir-Lab/DOMINO/issues/11
 - Use cache or reuse slices files from previous runs on the same network
+- Investigate why DOMINO does not build on amd64 after https://github.com/Reed-CompBio/spras/pull/235.
+
+## Versions
+
+- `v1`: Initial DOMINO container.
diff --git a/docker-wrappers/DOMINO/metadata.json b/docker-wrappers/DOMINO/metadata.json
new file mode 100644
index 000000000..4f2550474
--- /dev/null
+++ b/docker-wrappers/DOMINO/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "domino",
+    "architectures": ["linux/amd64"]
+}
diff --git a/docker-wrappers/MEO/Dockerfile b/docker-wrappers/MEO/Dockerfile
index 25b7ce32a..cb04907bd 100644
--- a/docker-wrappers/MEO/Dockerfile
+++ b/docker-wrappers/MEO/Dockerfile
@@ -1,6 +1,7 @@
 # Maximum Edge Orientation wrapper
 # https://github.com/agitter/meo/
 FROM amazoncorretto:8-alpine3.19
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /meo
 RUN export MEO_TAG=v1.1.0 && \
diff --git a/docker-wrappers/MEO/README.md b/docker-wrappers/MEO/README.md
index d6dfab5aa..602859e55 100644
--- a/docker-wrappers/MEO/README.md
+++ b/docker-wrappers/MEO/README.md
@@ -1,13 +1,13 @@
 # Maximum Edge Orientation Docker image
 
-A Docker image for [Maximum Edge Orientation](https://github.com/agitter/meo/) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/meo).
+A Docker image for [Maximum Edge Orientation](https://github.com/agitter/meo/) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/meo).
 Only supports the Random orientation algorithm, not MINSAT or MAXCSP.
 
 ## Building the Docker image
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/meo -f Dockerfile .
+docker build -t reed-compbio/meo -f Dockerfile .
 ```
 from this directory.
 
@@ -24,5 +24,5 @@ The Docker wrapper can be tested with `pytest`.
 
 ## Versions
 
-- `v1`: Initial version
+- `v1`: Initial MEO container
 - `v2`: Use `amazoncorretto` alpine base image
diff --git a/docker-wrappers/MEO/metadata.json b/docker-wrappers/MEO/metadata.json
new file mode 100644
index 000000000..9f9466c04
--- /dev/null
+++ b/docker-wrappers/MEO/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "meo",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/MinCostFlow/Dockerfile b/docker-wrappers/MinCostFlow/Dockerfile
index 9da359a62..20e80bfde 100644
--- a/docker-wrappers/MinCostFlow/Dockerfile
+++ b/docker-wrappers/MinCostFlow/Dockerfile
@@ -1,5 +1,6 @@
 #uses ubuntu as the base
 FROM python:3.10.7
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /MinCostFlow
 
diff --git a/docker-wrappers/MinCostFlow/README.md b/docker-wrappers/MinCostFlow/README.md
index 014a3d757..650af9d8f 100644
--- a/docker-wrappers/MinCostFlow/README.md
+++ b/docker-wrappers/MinCostFlow/README.md
@@ -1,20 +1,20 @@
 # MinCostFlow Docker image
 
-A Docker image for [MinCostFlow](https://github.com/gitter-lab/min-cost-flow) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/mincostflow).
+A Docker image for [MinCostFlow](https://github.com/gitter-lab/min-cost-flow) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/mincostflow).
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/mincostflow -f Dockerfile .
+docker build -t reed-compbio/mincostflow -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-docker run reedcompbio/mincostflow pip list
+docker run reed-compbio/mincostflow pip list
 ```
 or inspect the Python script arguments:
 ```
-docker run reedcompbio/mincostflow python /MinCostFlow/minCostFlow.py -h
+docker run reed-compbio/mincostflow python /MinCostFlow/minCostFlow.py -h
 ```
 Windows users may need to add the prefix `winpty` prefix before these commands.
 
@@ -30,9 +30,13 @@ The Docker wrapper can be tested with `pytest -k test_mcf.py` from the root of t
 
 Alternatively, to run the Docker image directly, run the following command from the root of the `spras` repository
 ```
-docker run -w /data --mount type=bind,source=/${PWD},target=/data reedcompbio/mincostflow python /MinCostFlow/minCostFlow.py --edges_file /data/test/MinCostFlow/input/graph1/edges.txt --sources_file /data/test/MinCostFlowinput/graph1/sources.txt --targets_file /data/test/MinCostFlowinput/graph1/targets.txt --flow 1 --output graph1 --capacity 1  
+docker run -w /data --mount type=bind,source=/${PWD},target=/data reed-compbio/mincostflow python /MinCostFlow/minCostFlow.py --edges_file /data/test/MinCostFlow/input/graph1/edges.txt --sources_file /data/test/MinCostFlowinput/graph1/sources.txt --targets_file /data/test/MinCostFlowinput/graph1/targets.txt --flow 1 --output graph1 --capacity 1  
 ```
 
 This will run MinCostFlow on the test input files and write the output files to the root of the `spras` repository.
 
 Windows users may need to escape the absolute paths so that `/data` becomes `//data`, etc.
+
+## Versions
+
+- `v1`: Initial MinCostFlow docker container.
diff --git a/docker-wrappers/MinCostFlow/metadata.json b/docker-wrappers/MinCostFlow/metadata.json
new file mode 100644
index 000000000..879d13a0f
--- /dev/null
+++ b/docker-wrappers/MinCostFlow/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "mincostflow",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/OmicsIntegrator1/README.md b/docker-wrappers/OmicsIntegrator1/README.md
index 43827327f..978df15d4 100644
--- a/docker-wrappers/OmicsIntegrator1/README.md
+++ b/docker-wrappers/OmicsIntegrator1/README.md
@@ -1,6 +1,6 @@
 # Omics Integrator 1 Docker image
 
-A Docker image for [Omics Integrator](https://github.com/fraenkel-lab/OmicsIntegrator) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/omics-integrator-1).
+A Docker image for [Omics Integrator](https://github.com/fraenkel-lab/OmicsIntegrator) that is available on the [GitHub Container Registry](https://github.com/Reed-CompBio/spras/pkgs/container/omics-integrator-1).
 
 ## Building and testing
 
diff --git a/docker-wrappers/OmicsIntegrator1/metadata.json b/docker-wrappers/OmicsIntegrator1/metadata.json
new file mode 100644
index 000000000..5118e928d
--- /dev/null
+++ b/docker-wrappers/OmicsIntegrator1/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "omics-integrator-1",
+    "architectures": ["linux/amd64"]
+}
diff --git a/docker-wrappers/OmicsIntegrator2/Dockerfile b/docker-wrappers/OmicsIntegrator2/Dockerfile
index 67ceb23a2..c6e3c1e3a 100644
--- a/docker-wrappers/OmicsIntegrator2/Dockerfile
+++ b/docker-wrappers/OmicsIntegrator2/Dockerfile
@@ -1,6 +1,7 @@
 # Omics Integrator 2 wrapper
 # https://github.com/fraenkel-lab/OmicsIntegrator2
 FROM continuumio/miniconda3:4.9.2
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 COPY 0001-disable-graph-exports.patch .
 
diff --git a/docker-wrappers/OmicsIntegrator2/README.md b/docker-wrappers/OmicsIntegrator2/README.md
index 881ce2d1f..f75e46627 100644
--- a/docker-wrappers/OmicsIntegrator2/README.md
+++ b/docker-wrappers/OmicsIntegrator2/README.md
@@ -1,19 +1,19 @@
 # Omics Integrator 2 Docker image
 
-A Docker image for [Omics Integrator 2](https://github.com/fraenkel-lab/OmicsIntegrator2) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/omics-integrator-2).
+A Docker image for [Omics Integrator 2](https://github.com/fraenkel-lab/OmicsIntegrator2) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/omics-integrator-2).
 
 ## Building the Docker image
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/omics-integrator-2 -f Dockerfile .
+docker build -t reed-compbio/omics-integrator-2 -f Dockerfile .
 ```
 from this directory.
 
 To confirm that commands are run inside the conda environment run:
 ```
-winpty docker run reedcompbio/omics-integrator-2 conda list
-winpty docker run reedcompbio/omics-integrator-2 OmicsIntegrator -h
+winpty docker run reed-compbio/omics-integrator-2 conda list
+winpty docker run reed-compbio/omics-integrator-2 OmicsIntegrator -h
 ```
 The `winpty` prefix is only needed on Windows.
 
@@ -31,3 +31,4 @@ The Docker wrapper can be tested with `pytest`.
 - Attribute https://github.com/fraenkel-lab/OmicsIntegrator2
 - Modify environment to use fraenkel-lab or [PyPI](https://pypi.org/project/OmicsIntegrator/) version instead of fork
 - Document usage
+- Use a different base image that is not `continuumio/miniconda3:4.9.2` to add arm64 support (see https://github.com/Reed-CompBio/spras/issues/315).
diff --git a/docker-wrappers/OmicsIntegrator2/metadata.json b/docker-wrappers/OmicsIntegrator2/metadata.json
new file mode 100644
index 000000000..2cdaf03d4
--- /dev/null
+++ b/docker-wrappers/OmicsIntegrator2/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "omics-integrator-2",
+    "architectures": ["linux/amd64"]
+}
diff --git a/docker-wrappers/PathLinker/Dockerfile b/docker-wrappers/PathLinker/Dockerfile
index 29950a059..272d389ba 100644
--- a/docker-wrappers/PathLinker/Dockerfile
+++ b/docker-wrappers/PathLinker/Dockerfile
@@ -1,6 +1,7 @@
 # PathLinker wrapper
 # https://github.com/Murali-group/PathLinker
 FROM python:3.5.10-alpine
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # gettext is required for the envsubst command
 # See https://github.com/haskell/cabal/issues/6126 regarding wget
diff --git a/docker-wrappers/PathLinker/README.md b/docker-wrappers/PathLinker/README.md
index a3e9aea49..3aff459ae 100644
--- a/docker-wrappers/PathLinker/README.md
+++ b/docker-wrappers/PathLinker/README.md
@@ -1,16 +1,16 @@
 # PathLinker Docker image
 
-A Docker image for [PathLinker](https://github.com/Murali-group/PathLinker) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/pathlinker).
+A Docker image for [PathLinker](https://github.com/Murali-group/PathLinker) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/pathlinker).
 
 To create the Docker image run:
 ```
-docker build -t reedcompbio/pathlinker -f Dockerfile .
+docker build -t reed-compbio/pathlinker -f Dockerfile .
 ```
 from this directory.
 
 To inspect the installed Python packages:
 ```
-winpty docker run reedcompbio/pathlinker pip list
+winpty docker run reed-compbio/pathlinker pip list
 ```
 The `winpty` prefix is only needed on Windows.
 
@@ -21,7 +21,7 @@ The Docker wrapper can be tested with `pytest`.
 
 Alternatively, to test the Docker image directly, run the following command from the root of the `spras` repository
 ```
-docker run -w /data --mount type=bind,source=/${PWD},target=/data reedcompbio/pathlinker python /PathLinker/run.py \
+docker run -w /data --mount type=bind,source=/${PWD},target=/data reed-compbio/pathlinker python /PathLinker/run.py \
   /data/test/PathLinker/input/sample-in-net.txt /data/test/PathLinker/input/sample-in-nodetypes.txt -k 5 --write-paths
 ```
 This will run PathLinker on the test input files and write the output files to the root of the `spras` repository.
diff --git a/docker-wrappers/PathLinker/metadata.json b/docker-wrappers/PathLinker/metadata.json
new file mode 100644
index 000000000..26f3db0ae
--- /dev/null
+++ b/docker-wrappers/PathLinker/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "pathlinker",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/README.md b/docker-wrappers/README.md
new file mode 100644
index 000000000..654b8adc2
--- /dev/null
+++ b/docker-wrappers/README.md
@@ -0,0 +1,31 @@
+# docker-wrappers
+
+This folder contains the list of all docker wrappers.
+
+We build these docker images with `buildx` to support multiple docker architectures.
+
+## `build.py`
+
+For convenience, we provide a `build.py` python file which pushes a docker image with the architectures
+that we want to support.
+
+```
+usage: build.py [-h] --dir DIR --version VERSION [--org-name ORG_NAME] [--yes | --no-yes] [--relax | --no-relax] [--push | --no-push] [--load | --no-load]
+build.py: error: the following arguments are required: --dir, --version
+```
+
+For example, using the default supported `ghcr.io` registry that SPRAS uses, we can build RWR v1:
+
+```sh
+docker login ghcr.io -u reed-compbio
+python build.py --dir RWR --version v1
+```
+
+> [!NOTE]
+> To use a docker image locally with this script, you must use `--load`. See below for more information.
+
+There are also two boolean settings:
+- `--push`: pushes the image to the GitHub Container Registry.
+- `--load`: loads the image into your local container registry. This only works with your system architecture, and multi-architecture builds can be tested by omitting `--load`.
+
+In general, use `--push` for production, `--load` for local development, and omit both to test the docker container on all architectures (which will happen on CI.)
diff --git a/docker-wrappers/RWR/Dockerfile b/docker-wrappers/RWR/Dockerfile
index d4772a7aa..206eb0c0c 100644
--- a/docker-wrappers/RWR/Dockerfile
+++ b/docker-wrappers/RWR/Dockerfile
@@ -1,4 +1,5 @@
 FROM python:3.11.5
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # Required for PageRank to run
 RUN pip install networkx==2.8.8 numpy==1.26.4 scipy==1.15.2
diff --git a/docker-wrappers/RWR/README.md b/docker-wrappers/RWR/README.md
index 9da37ac49..9e260968f 100644
--- a/docker-wrappers/RWR/README.md
+++ b/docker-wrappers/RWR/README.md
@@ -1,6 +1,6 @@
 # Source-Targets Random Walk with Restarts
 
-A Docker image for [RWR](https://github.com/Reed-CompBio/rwr) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/rwr).
+A Docker image for [RWR](https://github.com/Reed-CompBio/rwr) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/rwr).
 
 ## Notes
 The random walk with restarts algorithm requires a directed input network. However, the algorithm in its current form will accept an undirected input network and interpret it as a directed network. The resulting output from an undirected network does not accurately represent directionality.
@@ -9,10 +9,14 @@ The random walk with restarts algorithm requires a directed input network. Howev
 To build a new docker image for RWR navigate to the /docker-wrappers/rwr directory and enter:
 
 ```
-docker build -t reedcompbio/rwr -f Dockerfile .
+docker build -t reed-compbio/rwr -f Dockerfile .
 ```
 
 ## Testing
 Test code is located in `test/RWR`.
 The `input` subdirectory contains test files `rwr-network.txt`, `rwr-sources.txt`, and `rwr-targets.txt`
 The Docker wrapper can be tested with `pytest`.
+
+## Versions
+
+- v1: Initial version.
diff --git a/docker-wrappers/RWR/metadata.json b/docker-wrappers/RWR/metadata.json
new file mode 100644
index 000000000..196867c60
--- /dev/null
+++ b/docker-wrappers/RWR/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "rwr",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/ResponseNet/Dockerfile b/docker-wrappers/ResponseNet/Dockerfile
index ea7087590..a612f8780 100644
--- a/docker-wrappers/ResponseNet/Dockerfile
+++ b/docker-wrappers/ResponseNet/Dockerfile
@@ -1,5 +1,6 @@
 #uses ubuntu as the base
 FROM python:3.10.7
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 WORKDIR /ResponseNet
 
diff --git a/docker-wrappers/ResponseNet/README.md b/docker-wrappers/ResponseNet/README.md
index 5ca631527..2df23f2b9 100644
--- a/docker-wrappers/ResponseNet/README.md
+++ b/docker-wrappers/ResponseNet/README.md
@@ -1,3 +1,8 @@
 # ResponseNet Docker Image
 
-A Docker image for [ResponseNet](https://github.com/Reed-CompBio/ResponseNet) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/responsenet).
+A Docker image for [ResponseNet](https://github.com/Reed-CompBio/ResponseNet) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/responsenet).
+
+## Versions
+
+- v1: Initial version.
+- v2: Pin ResponseNet source code.
diff --git a/docker-wrappers/ResponseNet/metadata.json b/docker-wrappers/ResponseNet/metadata.json
new file mode 100644
index 000000000..f45aa6931
--- /dev/null
+++ b/docker-wrappers/ResponseNet/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "responsenet",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/SPRAS/Dockerfile b/docker-wrappers/SPRAS/Dockerfile
index 3d69943cc..b12b25ef4 100644
--- a/docker-wrappers/SPRAS/Dockerfile
+++ b/docker-wrappers/SPRAS/Dockerfile
@@ -1,4 +1,5 @@
 FROM almalinux:9
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # gcc/g++ are required for building several of the packages if you're using apple silicon
 RUN dnf update -y && \
diff --git a/docker-wrappers/SPRAS/README.md b/docker-wrappers/SPRAS/README.md
index 1cc3623d1..e56a8b0a1 100644
--- a/docker-wrappers/SPRAS/README.md
+++ b/docker-wrappers/SPRAS/README.md
@@ -1,5 +1,8 @@
 # SPRAS Docker image
 
+> [!NOTE]
+> All other containers are on the GitHub Container Registry. Until the next SPRAS release, the SPRAS docker image will remain on Docker Hub.
+
 ## Building Images
 
 A Docker image for SPRAS that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/spras)
diff --git a/docker-wrappers/SPRAS/example_config.yaml b/docker-wrappers/SPRAS/example_config.yaml
index 1e7fd69c2..754e7f299 100644
--- a/docker-wrappers/SPRAS/example_config.yaml
+++ b/docker-wrappers/SPRAS/example_config.yaml
@@ -24,10 +24,10 @@ containers:
   # Note that this assumes container names are consistent across registries, and that the
   # registry being passed doesn't require authentication for pull actions
   registry:
-    base_url: docker.io
+    base_url: ghcr.io
     # The owner or project of the registry
-    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
-    owner: reedcompbio
+    # For example, "reed-compbio" if the image is available as ghcr.io/reed-compbio/allpairs
+    owner: reed-compbio
 
 # This list of algorithms should be generated by a script which checks the filesystem for installs.
 # It shouldn't be changed by mere mortals. (alternatively, we could add a path to executable for each algorithm
diff --git a/docker-wrappers/SPRAS/metadata.json b/docker-wrappers/SPRAS/metadata.json
new file mode 100644
index 000000000..9bbbaf6e9
--- /dev/null
+++ b/docker-wrappers/SPRAS/metadata.json
@@ -0,0 +1,5 @@
+{
+    "imageName": "spras",
+    "architectures": ["linux/arm64", "linux/amd64"],
+    "cwd": "../../"
+}
diff --git a/docker-wrappers/ST_RWR/Dockerfile b/docker-wrappers/ST_RWR/Dockerfile
index cad7336d2..c8dd3df23 100644
--- a/docker-wrappers/ST_RWR/Dockerfile
+++ b/docker-wrappers/ST_RWR/Dockerfile
@@ -1,4 +1,5 @@
 FROM python:3.11.5
+LABEL org.opencontainers.image.source=https://github.com/Reed-CompBio/spras
 
 # Required for PageRank to run
 RUN pip install networkx==2.8.8 numpy==1.26.4 scipy==1.15.2
diff --git a/docker-wrappers/ST_RWR/README.md b/docker-wrappers/ST_RWR/README.md
index 97ee7391f..5bc10623c 100644
--- a/docker-wrappers/ST_RWR/README.md
+++ b/docker-wrappers/ST_RWR/README.md
@@ -1,6 +1,6 @@
 # Source-Targets Random Walk with Restarts
 
-A Docker image for [ST-RWR](https://github.com/Reed-CompBio/rwr) that is available on [DockerHub](https://hub.docker.com/repository/docker/reedcompbio/st_rwr).
+A Docker image for [ST-RWR](https://github.com/Reed-CompBio/rwr) that is available on the [GitHub Container Registry](https://github.com/orgs/Reed-CompBio/packages/container/package/st_rwr).
 
 ## Notes
 The random walk with restarts algorithm requires a directed input network. However, the algorithm in its current form will accept an undirected input network and interpret it as a directed network. The resulting output from an undirected network does not accurately represent directionality.
@@ -9,10 +9,14 @@ The random walk with restarts algorithm requires a directed input network. Howev
 To build a new docker image for ST_RWR navigate to the /docker-wrappers/ST_RWR directory and enter:
 
 ```
-docker build -t reedcompbio/str-wr -f Dockerfile .
+docker build -t reed-compbio/st-rwr -f Dockerfile .
 ```
 
 ## Testing
 Test code is located in `test/ST_RWR`.
 The `input` subdirectory contains test files `strwr-network.txt`, `strwr-sources.txt`, and `strwr-targets.txt`
-The Docker wrapper can be tested with `pytest`.
\ No newline at end of file
+The Docker wrapper can be tested with `pytest`.
+
+## Versions
+
+- v1: Initial version.
diff --git a/docker-wrappers/ST_RWR/metadata.json b/docker-wrappers/ST_RWR/metadata.json
new file mode 100644
index 000000000..66ac0f212
--- /dev/null
+++ b/docker-wrappers/ST_RWR/metadata.json
@@ -0,0 +1,4 @@
+{
+    "imageName": "st-rwr",
+    "architectures": ["linux/arm64", "linux/amd64"]
+}
diff --git a/docker-wrappers/build.py b/docker-wrappers/build.py
new file mode 100644
index 000000000..66d88f719
--- /dev/null
+++ b/docker-wrappers/build.py
@@ -0,0 +1,120 @@
+import argparse
+import json
+import os
+import subprocess
+from pathlib import Path
+
+COMMAND_BUILDX = ["docker", "buildx"]
+
+COMMAND_BUILDER_LS = COMMAND_BUILDX + ["ls"]
+COMMAND_BUILDER_INSTANCE = COMMAND_BUILDX + ["create", "--name", "container", "--driver=docker-container"]
+
+# https://stackoverflow.com/a/5137509/7589775
+dir_path = os.path.dirname(os.path.realpath(__file__))
+
+def construct_push_command(
+    tags: list[str],
+    dir: str,
+    architectures: list[str],
+    push: bool,
+    load: bool
+) -> list[str]:
+    """
+    Constructs the docker command to be run by this script
+    """
+    base_cmd = ["build"]
+    for tag in tags:
+        base_cmd.extend(["--tag", tag])
+
+    if push and load:
+        raise RuntimeError("You specified both container pushing and container loading. Did you mean to test the container first?")
+
+    base_cmd = base_cmd + [
+        "--file",
+        str(Path(dir_path, dir, "Dockerfile"))]
+
+    if not load:
+        # Add the architectures if load is not specified.
+        base_cmd = base_cmd + ["--platform", ",".join(architectures)]
+
+    base_cmd = base_cmd + ["--builder", "container"]
+
+    if push: base_cmd.append("--push")
+    if load: base_cmd.append("--load")
+
+    # The 'local' directory: the CWD is set by the python code
+    # running this function's output command.
+    base_cmd.append(".")
+
+    return COMMAND_BUILDX + base_cmd
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(
+        description="Docker Wrapper builder python wrapper"
+    )
+    parser.add_argument("--dir", type=str, required=True, help="The directory of the docker wrapper to use")
+    parser.add_argument("--version", type=str, required=True, help="The version (tag name) to use for the container")
+    parser.add_argument("--org-name", type=str, help="The organization to push to", default="ghcr.io/reed-compbio/")
+    parser.add_argument("--yes", type=bool, help="Whether to automatically agree to pushing a container", action=argparse.BooleanOptionalAction)
+    parser.add_argument("--relax", type=bool, help="Whether to not be strict on tag naming (this requires all versions start with `v`.)", action=argparse.BooleanOptionalAction)
+    parser.add_argument("--push", type=bool, help="Enabling push pushes the image. Usually, images are only built locally.", action=argparse.BooleanOptionalAction)
+    # This is a (sensible) limitation of docker: https://github.com/docker/buildx/issues/59. We don't say what architecture we want
+    # to default to the system architecture.
+    parser.add_argument("--load", type=bool, help="Enabling load adds a docker image to your local machine. This uses your local architecture.", action=argparse.BooleanOptionalAction)
+
+    return parser.parse_args()
+
+def main():
+    # We need a buildx environment
+    # This is a terrible check. Yes, docker buildx has no API exposed on docker-py.
+    if f"\ncontainer" not in subprocess.check_output(COMMAND_BUILDER_LS).decode("utf-8"):
+        out = subprocess.run(COMMAND_BUILDER_INSTANCE)
+        if out.returncode != 0:
+            raise RuntimeError(f"Command {COMMAND_BUILDER_INSTANCE} exited with non-zero exit code.")
+
+    args = parse_arguments()
+
+    if not args.org_name.endswith("/"):
+        args.org_name = f"{args.org_name}/"
+
+    if not args.version.startswith("v"):
+        if not args.relax:
+            raise ValueError("All versions start with v (v1, v2, ...)")
+
+    metadata_path = Path(dir_path, args.dir, "metadata.json")
+    metadata = json.loads(metadata_path.read_text())
+    name = metadata['imageName']
+    architectures = metadata['architectures']
+
+    assert len(architectures) > 0, "you must specify at least one container architecture!"
+
+    cwd = str(Path(dir_path, args.dir, metadata['cwd']) if 'cwd' in metadata else Path(dir_path, args.dir))
+    tag = args.org_name + name + ":" + args.version
+    tag_latest = args.org_name + name + ":latest"
+
+    if args.load:
+        print(f"Building {name} only on the system architecture with:")
+    else:
+        print(f"Building {name} over {architectures} with:")
+    print(f"- CWD: {cwd}")
+    print(f"- Specified tag: {tag}")
+    print(f"-    Latest tag: {tag_latest}\n")
+    if args.push:
+        print("The docker images with the above tags will be _pushed_. (This command will also test all provided architectures beforehand.)")
+    elif args.load:
+        print("The docker images with the above tags will be _loaded_. This command will not test all provided architectures. To test, omit --load.")
+    else:
+        print("The docker images with the above tags will be _tested_. This command will not push (use --push) or allow this image to be used locally (use --load)")
+    if not args.yes:
+        confirm_string = "[y/n] Are you sure you want to do this? "
+        confirm = input(confirm_string)
+        if confirm.strip().lower() not in ('y', 'yes'):
+            raise RuntimeError("Did not confirm dialog.")
+
+    push_command = construct_push_command([tag, tag_latest], args.dir, architectures, push=args.push, load=args.load)
+    result = subprocess.run(push_command, capture_output=False, cwd=cwd)
+
+    exit(result.returncode)
+
+if __name__ == '__main__':
+    main()
diff --git a/docs/contributing/index.rst b/docs/contributing/index.rst
index b0780619f..d1f2087cc 100644
--- a/docs/contributing/index.rst
+++ b/docs/contributing/index.rst
@@ -20,7 +20,6 @@ Snakemake workflow. Before following this guide, a contributor will need
   introduction <https://swcarpentry.github.io/git-novice/>`__)
 - Familiarity with Docker and Dockerfiles to create images (`Carpentries
   introduction <https://carpentries-incubator.github.io/docker-introduction/>`__)
-- A `Docker Hub <https://hub.docker.com/>`__ account
 
 It is not necessary to have experience with Snakemake, Python testing,
 or pandas before getting started, but it may help with more complex
@@ -129,10 +128,10 @@ Build the Docker image by running
 
 ::
 
-   docker build -t <username>/local-neighborhood -f Dockerfile .
+   python3 ../build.py --dir LocalNeighborhood --version latest --org-name <username>
 
 from the ``LocalNeighborhood`` directory, where ``<username>`` is your
-Docker Hub username. Docker must be running on your system before
+GitHub username. Docker must be running on your system before
 executing this command.
 
 Test the image by running it with the example input files
@@ -158,15 +157,6 @@ have already been copied into the current working directory. Windows
 users may need to escape the absolute paths so that ``/data`` becomes
 ``//data``, etc. Confirm that the output file matches expectations.
 
-Push the new image to Docker Hub:
-
-::
-
-   docker push <username>/local-neighborhood
-
-Pushing an image requires being logged in, so run ``docker login`` first
-if needed using your Docker Hub username and password.
-
 Step 3: Write the Local Neighborhood wrapper functions
 ------------------------------------------------------
 
@@ -284,10 +274,9 @@ Local Neighborhood has no other parameters. Optionally set
 make testing faster.
 
 The config file has an option ``owner`` under the ``containers.registry``
-settings that controls which Docker Hub account will be used when
-pulling Docker images. The same Docker Hub account will be used for all
-images and cannot currently be set different for each algorithm. Set the
-``owner`` to match your Docker Hub username from Step 2.
+settings that controls which container registry account will be used when
+pulling Docker images. The same container registry account will be used for all
+images and cannot currently be set different for each algorithm.
 
 After completing this step, try running the Local Neighborhood algorithm
 through SPRAS with
@@ -331,8 +320,8 @@ the pytest testing.
 Extend ``.github/workflows/build-containers.yml`` to pull and build the
 new Docker image. Follow the example for any of the other pathway
 reconstruction algorithm. First pull the image
-``<username>/local-neighborhood`` from Docker Hub. Then build the Docker
-image using the ``Dockerfile`` that was completed in Step 2.
+``<username>/local-neighborhood`` from the GitHub Container Registry.
+Then build the Docker image using the ``Dockerfile`` that was completed in Step 2.
 
 Modify generate inputs:
 
@@ -419,7 +408,7 @@ General steps for contributing a new pathway reconstruction algorithm
     ``<algorithm>``, and include any other files required to build that
     image in the subdirectory
 3.  Build and push the Docker image to the
-    `reedcompbio <https://hub.docker.com/orgs/reedcompbio>`__ Docker
+    `reed-compbio <https://github.com/orgs/Reed-CompBio/packages/>`__ GitHub
     organization (SPRAS maintainer required)
 4.  Add a new Python file ``spras/<algorithm>.py`` to implement the
     wrapper functions for ``<algorithm>``: specify the list of
diff --git a/docs/install.rst b/docs/install.rst
index bc399b36a..d2a9e1a1b 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -26,16 +26,16 @@ You can also install SPRAS as a package using `pip` directly from the github rep
 Getting the SPRAS Docker Image
 ------------------------------
 SPRAS also publishes a Docker image that already holds all the necessary dependencies. Assuming you have Docker installed, you can pull
-the image from Docker Hub:
+the image from the GitHub Container Registry:
 
 .. code-block:: bash
 
-    docker pull reedcompbio/spras:latest
+    docker pull ghcr.io/reed-compbio/spras:latest
 
 If you want to pull a specific version of spras, use the version for the image tag name. For example, to get spras v0.6.0:
 
 .. code-block:: bash
 
-    docker pull reedcompbio/spras:0.6.0
+    docker pull ghcr.io/reed-compbio/spras:0.6.0
 
 .. _Download and Install Conda: https://conda-forge.org/download/
\ No newline at end of file
diff --git a/spras/allpairs.py b/spras/allpairs.py
index 21fca6ee4..15ce43e3c 100644
--- a/spras/allpairs.py
+++ b/spras/allpairs.py
@@ -103,7 +103,7 @@ def run(inputs, output_file, args=None, container_settings=None):
         if Path(inputs["directed_flag"]).read_text().strip() == "true":
             command.append("--directed")
 
-        container_suffix = "allpairs:v4"
+        container_suffix = "allpairs:v3"
         run_container_and_log(
             'All Pairs Shortest Paths',
             container_suffix,
diff --git a/spras/analysis/cytoscape.py b/spras/analysis/cytoscape.py
index e84899506..6edb70117 100644
--- a/spras/analysis/cytoscape.py
+++ b/spras/analysis/cytoscape.py
@@ -48,7 +48,7 @@ def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, contai
         # Provided the mapped pathway file path and the original file path as the label Cytoscape
         command.extend(['--pathway', f'{mapped_pathway}|{pathway}'])
 
-    container_suffix = "py4cytoscape:v3"
+    container_suffix = "py4cytoscape:v1"
     run_container_and_log('Cytoscape',
                          container_suffix,
                          command,
diff --git a/spras/config/container_schema.py b/spras/config/container_schema.py
index c4f293107..3e36b0381 100644
--- a/spras/config/container_schema.py
+++ b/spras/config/container_schema.py
@@ -13,7 +13,7 @@
 
 from spras.config.util import CaseInsensitiveEnum
 
-DEFAULT_CONTAINER_PREFIX = "docker.io/reedcompbio"
+DEFAULT_CONTAINER_PREFIX = "ghcr.io/reed-compbio"
 
 class ContainerFramework(CaseInsensitiveEnum):
     docker = 'docker'
@@ -69,7 +69,7 @@ def from_container_settings(settings: ContainerSettings, hash_length: int) -> "P
             warnings.warn("unpack_singularity is set to True, but the container framework is not singularity. This setting will have no effect.", stacklevel=2)
         unpack_singularity = settings.unpack_singularity
 
-        # Grab registry from the config, and if none is provided default to docker
+        # Grab registry from the config, and if none is provided default to GHCR
         container_prefix = DEFAULT_CONTAINER_PREFIX
         if settings.registry and settings.registry.base_url != "" and settings.registry.owner != "":
             container_prefix = settings.registry.base_url + "/" + settings.registry.owner
diff --git a/spras/domino.py b/spras/domino.py
index 316044432..5debc3360 100644
--- a/spras/domino.py
+++ b/spras/domino.py
@@ -113,7 +113,7 @@ def run(inputs, output_file, args=None, container_settings=None):
                           '--network_file', network_file,
                           '--output_file', mapped_slices_file]
 
-        container_suffix = "domino"
+        container_suffix = "domino:v1"
         try:
             run_container_and_log('slicer',
                                 container_suffix,
diff --git a/spras/mincostflow.py b/spras/mincostflow.py
index dad1d706c..0c3f1514a 100644
--- a/spras/mincostflow.py
+++ b/spras/mincostflow.py
@@ -118,7 +118,7 @@ def run(inputs, output_file, args=None, container_settings=None):
             command.extend(['--capacity', str(args.capacity)])
 
         # choosing to run in docker or singularity container
-        container_suffix = "mincostflow"
+        container_suffix = "mincostflow:v1"
 
         # constructs a docker run call
         run_container_and_log('MinCostFlow',
diff --git a/test/analysis/input/config.yaml b/test/analysis/input/config.yaml
index f16c1dbc7..df7da73d3 100644
--- a/test/analysis/input/config.yaml
+++ b/test/analysis/input/config.yaml
@@ -4,8 +4,8 @@ containers:
   framework: docker
   unpack_singularity: false
   registry:
-    base_url: docker.io
-    owner: reedcompbio
+    base_url: ghcr.io
+    owner: reed-compbio
 
 algorithms:
   - name: "pathlinker"
diff --git a/test/analysis/input/egfr.yaml b/test/analysis/input/egfr.yaml
index 823db03bb..90634a272 100644
--- a/test/analysis/input/egfr.yaml
+++ b/test/analysis/input/egfr.yaml
@@ -22,10 +22,10 @@ containers:
   # Note that this assumes container names are consistent across registries, and that the
   # registry being passed doesn't require authentication for pull actions
   registry:
-    base_url: docker.io
+    base_url: ghcr.io
     # The owner or project of the registry
-    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
-    owner: reedcompbio
+    # For example, "reed-compbio" if the image is available as ghcr.io/reed-compbio/allpairs
+    owner: reed-compbio
 
 algorithms:
   - name: pathlinker
diff --git a/test/generate-inputs/inputs/test_config.yaml b/test/generate-inputs/inputs/test_config.yaml
index 5638d5cc2..54cec40ff 100644
--- a/test/generate-inputs/inputs/test_config.yaml
+++ b/test/generate-inputs/inputs/test_config.yaml
@@ -3,8 +3,8 @@ containers:
   framework: docker
   unpack_singularity: false
   registry:
-    base_url: docker.io
-    owner: reedcompbio
+    base_url: ghcr.io
+    owner: reed-compbio
 
 algorithms:
   - name: "pathlinker"
diff --git a/test/test_config.py b/test/test_config.py
index 41551c381..9cc88c52f 100644
--- a/test/test_config.py
+++ b/test/test_config.py
@@ -27,8 +27,8 @@ def get_test_config():
         "containers": {
             "framework": "singularity",
             "registry": {
-                "base_url": "docker.io",
-                "owner": "reedcompbio",
+                "base_url": "ghcr.io",
+                "owner": "reed-compbio",
             },
         },
         "hash_length": 7,
@@ -203,6 +203,7 @@ def test_config_container_framework_normalization(self):
 
     def test_config_container_registry(self):
         test_config = get_test_config()
+        # docker.io/reedcompbio was our old container registry.
         test_config["containers"]["registry"]["base_url"] = "docker.io"
         test_config["containers"]["registry"]["owner"] = "reedcompbio"
         config.init_global(test_config)