diff --git a/.github/workflows/conda_env_check.yml b/.github/workflows/conda_env_check.yml
deleted file mode 100644
index 796fe6c..0000000
--- a/.github/workflows/conda_env_check.yml
+++ /dev/null
@@ -1,27 +0,0 @@
-name: Check Conda Envs
-
-on:
-  pull_request:
-    branches: [ main, master ]
-  push:
-    branches: [ main, master ]
-  workflow_dispatch:
-    inputs:
-      envs:
-        description: 'Regex for envs'     
-        required: false
-        default: 'envs/'
-
-jobs:
-  check_conda_envs:
-    name: Check Conda Envs
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v4
-      
-      - name: Check Conda Envs
-        uses: Ulthran/conda_env_check@v1
-        with:
-          envs: "envs/"
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
new file mode 100644
index 0000000..3e7164e
--- /dev/null
+++ b/.github/workflows/docker.yml
@@ -0,0 +1,60 @@
+name: Push to DockerHub
+
+on:
+  workflow_call:
+
+  workflow_dispatch:
+
+jobs:
+    build-and-push-to-dockerhub:
+        name: Push Docker image to Docker Hub
+        runs-on: ubuntu-latest
+    
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v4
+            
+            - name: Get sbx version
+              shell: bash
+              run: |
+                SBX_VER=$(cat VERSION)
+                echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
+            
+            - name: Log in to Docker Hub
+              uses: docker/login-action@v3
+              with:
+                username: ${{ secrets.DOCKERHUB_USERNAME }}
+                password: ${{ secrets.DOCKERHUB_TOKEN }}
+            
+            - name: Extract metadata (tags, labels) for Docker
+              id: meta
+              uses: docker/metadata-action@v5
+              with:
+                images: sunbeamlabs/sbx_assembly
+            
+            - name: Build and push Docker image for annotation
+              uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: envs/sbx_annotation.Dockerfile
+                push: true
+                tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-annotation
+                labels: ${{ steps.meta.outputs.labels }}
+
+            - name: Build and push Docker image for assembly
+              uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: envs/sbx_assembly.Dockerfile
+                push: true
+                tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-assembly
+                labels: ${{ steps.meta.outputs.labels }}
+
+            - name: Build and push Docker image for coverage
+              uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: envs/sbx_coverage.Dockerfile
+                push: true
+                tags: sunbeamlabs/sbx_assembly:${{ env.SBX_VER }}-coverage
+                labels: ${{ steps.meta.outputs.labels }}
\ No newline at end of file
diff --git a/.github/workflows/linter.yml b/.github/workflows/linter.yml
deleted file mode 100755
index 867df5a..0000000
--- a/.github/workflows/linter.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-name: Super-Linter
-
-on:
-  pull_request:
-    branches: [ master, main ]
-  push:
-    branches: [ master, main ]
-
-jobs:
-  lint:
-    name: Lint Code Base
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout Code
-        uses: actions/checkout@v3
-
-      - name: Lint Code Base
-        uses: github/super-linter@v4
-        env:
-          VALIDATE_ALL_CODEBASE: true
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-          VALIDATE_SNAKEMAKE_SNAKEFMT: true
-          VALIDATE_PYTHON_BLACK: true
\ No newline at end of file
diff --git a/.github/workflows/pr.yml b/.github/workflows/pr.yml
new file mode 100644
index 0000000..ed35a2b
--- /dev/null
+++ b/.github/workflows/pr.yml
@@ -0,0 +1,12 @@
+name: Tests
+
+on:
+    pull_request:
+      branches:
+        - main
+
+jobs:
+    run-tests:
+        uses: ./.github/workflows/tests.yml
+        secrets: inherit
+    
\ No newline at end of file
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..2db6d23
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,79 @@
+name: Release
+
+on:
+    release:
+      types: [published]
+
+    workflow_dispatch:
+
+jobs:
+    run-tests:
+        uses: ./.github/workflows/tests.yml
+        secrets: inherit
+
+    check-version:
+        runs-on: ubuntu-latest
+        steps:
+          - name: Checkout
+            uses: actions/checkout@v4
+          
+          - name: Get sbx version
+            shell: bash
+            run: |
+              SBX_VER=$(cat VERSION)
+              echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
+
+          - id: get_version
+            uses: battila7/get-version-action@v2
+
+          - name: Check version
+            shell: bash
+            run: |
+              RELEASE_VERSION=${{ steps.get_version.outputs.version-without-v }}
+              echo "Release version: ${RELEASE_VERSION}"
+              echo "Sbx version: ${{ env.SBX_VER }}"
+
+              if [[ $RELEASE_VERSION == ${{ env.SBX_VER }} ]]; then
+                  echo "Versions match, continuing..."
+              else
+                  echo "Versions don't match, exiting..."
+                  exit 1
+              fi
+
+    push-to-dockerhub:
+        uses: ./.github/workflows/docker.yml
+        secrets: inherit
+        needs:
+          - run-tests
+          - check-version
+    
+    test-apptainer:
+      name: Apptainer Test
+      runs-on: ubuntu-latest
+      needs: push-to-dockerhub
+  
+      steps:
+        - name: Checkout Code
+          uses: actions/checkout@v4
+
+        - name: Set test env
+          run: echo "SUNBEAM_TEST_PROFILE=apptainer" >> $GITHUB_ENV
+
+        - uses: eWaterCycle/setup-apptainer@v2
+          with:
+            apptainer-version: 1.1.2
+          
+        - name: Test with Sunbeam
+          uses: sunbeam-labs/sbx_test_action@v1
+          with:
+            test-directory: ".tests/e2e/"
+  
+        - name: Dump Logs
+          shell: bash
+          if: always()
+          run: tail -n +1 logs/*
+        
+        - name: Dump Stats
+          shell: bash
+          if: always()
+          run: cat stats/*
\ No newline at end of file
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 30cc75e..2df6a4c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,31 +1,73 @@
 name: Tests
 
 on:
-  pull_request:
-    branches: [ master, main ]
   push:
     branches: [ master, main ]
+  workflow_call:
+  workflow_dispatch:
   schedule:
     - cron: "0 13 * * 1"
 
-jobs:  
+jobs:
+  lint:
+    name: Lint Code
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+      
+      - uses: actions/setup-python@v5
+        with:
+            python-version: 3.12
+
+      - name: Install Dependencies
+        run: pip install black snakefmt
+
+      - name: Run Linter
+        run: |
+          black --check .
+          snakefmt --check *.smk
+
+  test-unit:
+    name: Run Extension Unit Tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+      
+      - uses: actions/setup-python@v5
+        with:
+            python-version: 3.12
+      
+      - name: Install Dependencies
+        run: pip install pytest
+
+      - name: Run Unit Tests
+        run: true #pytest .tests/unit/
+        # This'll require having a lib within scripts with internal tests
+
   test-e2e:
     name: Test Extension with Sunbeam
     runs-on: ubuntu-latest
+    needs:
+      - test-unit
+      - lint
 
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         
       - name: Test with Sunbeam
         uses: sunbeam-labs/sbx_test_action@v1
-          
-      - name: Dump Logs
-        shell: bash
-        if: always()
-        run: tail -n +1 logs/*
+
+      #- name: Dump Logs
+      #  shell: bash
+      #  if: always()
+      #  run: tail -n +1 logs/*
       
-      - name: Dump Stats
-        shell: bash
-        if: always()
-        run: cat stats/*
+      #- name: Dump Stats
+      #  shell: bash
+      #  if: always()
+      #  run: cat stats/*
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ed8ebf5
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+__pycache__
\ No newline at end of file
diff --git a/.tests/test_megahit.sh b/.tests/test_megahit.sh
deleted file mode 100755
index f03d6f2..0000000
--- a/.tests/test_megahit.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-# Fix for #167:
-# Check that if megahit gives a nonzero exit code it is handled appropriately.
-# The two main cases are 255 (empty contigs) and anything else nonzero
-# (presumed to be memory-related in the assembly rules).
-# Checking for successful behavior is already handled in test_all.
-function test_assembly_failures {
-    # Up to just before the assembly rules, things should work fine.
-    sunbeam run --profile $TEMPDIR/ all_decontam --configfile=$TEMPDIR/tmp_config.yml
-    # Remove previous assembly files, if they exist.
-    rm -rf $TEMPDIR/sunbeam_output/assembly
-
-    # If megahit exits with 255, it implies no contigs were built.
-#    mkdir -p "$TEMPDIR/megahit_255"
-#    echo -e '#!/usr/bin/env bash\nexit 255' > $TEMPDIR/megahit_255/megahit
-#    chmod +x $TEMPDIR/megahit_255/megahit
-#    (
-#    export PATH="$TEMPDIR/megahit_255:$PATH"
-#    txt=$(sunbeam run -- --configfile=$TEMPDIR/tmp_config.yml -p all_assembly)
-#    echo "$txt" > /mnt/d/Penn/sunbeam/log.txt
-#    echo "$txt" | grep "Empty contigs"
-#    )
-
-    # If megahit gives an exit code != 0 and != 255 it is an error.
-    mkdir -p "$TEMPDIR/megahit_137"
-    echo -e '#!/usr/bin/env bash\nexit 137' > $TEMPDIR/megahit_137/megahit
-    chmod +x $TEMPDIR/megahit_137/megahit
-    (
-    export PATH="$TEMPDIR/megahit_137:$PATH"
-    # (This command should *not* exit successfully.)
-    ! txt=$(sunbeam run --profile $TEMPDIR/ all_assembly --configfile=$TEMPDIR/tmp_config.yml)
-    echo "$txt" | grep "Check your memory"
-    )
-}
\ No newline at end of file
diff --git a/README.md b/README.md
index 50fc21b..f7fbb7b 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 
 <!-- Begin badges -->
 [![Tests](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/tests.yml)
-[![Super-Linter](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/linter.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_assembly/actions/workflows/linter.yml)
+[![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_assembly)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_assembly/)
 <!-- End badges -->
 
 A [Sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for assembly of contigs using Megahit, gene annotation using Prodigal, and annotation using [Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi) and [Diamond](https://github.com/bbuchfink/diamond). It can also map reads to contigs and calculat per-base coverage using [Minimap2](https://github.com/lh3/minimap2) and [samtools](https://github.com/samtools/samtools).
diff --git a/VERSION b/VERSION
new file mode 100644
index 0000000..bd52db8
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+0.0.0
\ No newline at end of file
diff --git a/envs/sbx_annotation.Dockerfile b/envs/sbx_annotation.Dockerfile
new file mode 100644
index 0000000..1011efe
--- /dev/null
+++ b/envs/sbx_annotation.Dockerfile
@@ -0,0 +1,17 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_assembly_env
+
+COPY envs/sbx_annotation.yml ./
+
+# Install environment
+RUN mamba env create --file sbx_annotation.yml --name sbx_annotation
+
+ENV PATH="/opt/conda/envs/sbx_annotation/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "sbx_annotation", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"
\ No newline at end of file
diff --git a/envs/sbx_assembly.Dockerfile b/envs/sbx_assembly.Dockerfile
new file mode 100644
index 0000000..9012d53
--- /dev/null
+++ b/envs/sbx_assembly.Dockerfile
@@ -0,0 +1,17 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_assembly_env
+
+COPY envs/sbx_assembly.yml ./
+
+# Install environment
+RUN mamba env create --file sbx_assembly.yml --name sbx_assembly
+
+ENV PATH="/opt/conda/envs/sbx_assembly/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "sbx_assembly", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"
\ No newline at end of file
diff --git a/envs/sbx_coverage.Dockerfile b/envs/sbx_coverage.Dockerfile
new file mode 100644
index 0000000..07b765c
--- /dev/null
+++ b/envs/sbx_coverage.Dockerfile
@@ -0,0 +1,17 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_assembly_env
+
+COPY envs/sbx_coverage.yml ./
+
+# Install environment
+RUN mamba env create --file sbx_coverage.yml --name sbx_coverage
+
+ENV PATH="/opt/conda/envs/sbx_coverage/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "sbx_coverage", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"
\ No newline at end of file
diff --git a/envs/sbx_coverage.yml b/envs/sbx_coverage.yml
index d552836..72db8e4 100644
--- a/envs/sbx_coverage.yml
+++ b/envs/sbx_coverage.yml
@@ -6,4 +6,4 @@ dependencies:
   - minimap2
   - numpy
   - samtools=1.9
-  - python>3
\ No newline at end of file
+  - python=3
\ No newline at end of file
diff --git a/sbx_annotation.smk b/sbx_annotation.smk
index 402d6c8..49804b6 100644
--- a/sbx_annotation.smk
+++ b/sbx_annotation.smk
@@ -9,6 +9,18 @@ from sunbeamlib.config import makepath, verify
 TARGET_ANNOTATE = ANNOTATION_FP / "all_samples.tsv"
 
 
+def get_assembly_ext_path() -> Path:
+    ext_path = Path(sunbeam_dir) / "extensions" / "sbx_assembly"
+    if ext_path.exists():
+        return ext_path
+    raise Error(
+        "Filepath for assembly not found, are you sure it's installed under extensions/sbx_assembly?"
+    )
+
+
+SBX_ASSEMBLY_VERSION = open(get_assembly_ext_path() / "VERSION").read().strip()
+
+
 try:
     BENCHMARK_FP
 except NameError:
@@ -55,6 +67,8 @@ rule build_diamond_db:
         LOG_FP / "build_diamond_db.log",
     conda:
         "envs/sbx_annotation.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-annotation"
     shell:
         """
         diamond makedb --in {input} -d {input} 2>&1 | tee {log}
@@ -76,6 +90,8 @@ rule run_blastn:
     threads: Cfg["sbx_annotation"]["threads"]
     conda:
         "envs/sbx_annotation.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-annotation"
     shell:
         """
         blastn \
@@ -104,6 +120,8 @@ rule run_diamond_blastp:
     threads: Cfg["sbx_annotation"]["threads"]
     conda:
         "envs/sbx_annotation.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-annotation"
     shell:
         """
         if [ -s {input.genes} ]; then
@@ -137,6 +155,8 @@ rule run_diamond_blastx:
     threads: Cfg["sbx_annotation"]["threads"]
     conda:
         "envs/sbx_annotation.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-annotation"
     shell:
         """
         if [ -s {input.genes} ]; then
@@ -167,6 +187,8 @@ rule blast_report:
         ANNOTATION_FP / "{blast_prog}" / "{db}" / "{query}" / "report.tsv",
     conda:
         "envs/sbx_annotation.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-annotation"
     script:
         "scripts/blast_report.py"
 
@@ -213,6 +235,8 @@ rule aggregate_results:
         prot=Blastdbs["prot"],
     conda:
         "envs/sbx_annotation.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-annotation"
     script:
         "scripts/aggregate_results.py"
 
diff --git a/sbx_assembly.smk b/sbx_assembly.smk
index a52ec35..ee68b3a 100644
--- a/sbx_assembly.smk
+++ b/sbx_assembly.smk
@@ -15,6 +15,18 @@ TARGET_ASSEMBLY = [
 ]
 
 
+def get_assembly_ext_path() -> Path:
+    ext_path = Path(sunbeam_dir) / "extensions" / "sbx_assembly"
+    if ext_path.exists():
+        return ext_path
+    raise Error(
+        "Filepath for assembly not found, are you sure it's installed under extensions/sbx_assembly?"
+    )
+
+
+SBX_ASSEMBLY_VERSION = open(get_assembly_ext_path() / "VERSION").read().strip()
+
+
 try:
     BENCHMARK_FP
 except NameError:
@@ -49,6 +61,8 @@ rule megahit_paired:
     threads: 4
     conda:
         "envs/sbx_assembly.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-assembly"
     shell:
         """
         ## turn off bash strict mode
@@ -88,6 +102,8 @@ rule megahit_unpaired:
     threads: 4
     conda:
         "envs/sbx_assembly.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-assembly"
     shell:
         """
         ## turn off bash strict mode
@@ -146,6 +162,8 @@ rule prodigal:
         LOG_FP / "prodigal_{sample}.log",
     conda:
         "envs/sbx_assembly.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-assembly"
     shell:
         """
         if [[ -s {input} ]]; then
diff --git a/sbx_coverage.smk b/sbx_coverage.smk
index fbab43d..9360cbe 100644
--- a/sbx_coverage.smk
+++ b/sbx_coverage.smk
@@ -4,6 +4,18 @@
 #
 # Requires Minimap2 and samtools.
 
+
+def get_assembly_ext_path() -> Path:
+    ext_path = Path(sunbeam_dir) / "extensions" / "sbx_assembly"
+    if ext_path.exists():
+        return ext_path
+    raise Error(
+        "Filepath for assembly not found, are you sure it's installed under extensions/sbx_assembly?"
+    )
+
+
+SBX_ASSEMBLY_VERSION = open(get_assembly_ext_path() / "VERSION").read().strip()
+
 try:
     BENCHMARK_FP
 except NameError:
@@ -48,6 +60,8 @@ rule minimap_alignment:
     threads: Cfg["sbx_coverage"]["threads"]
     conda:
         "envs/sbx_coverage.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-coverage"
     shell:
         """
         minimap2 -ax sr -t {threads} {input.contig} {input.reads} 1> {output} 2> {log}
@@ -66,6 +80,8 @@ rule contigs_sort:
     threads: Cfg["sbx_coverage"]["threads"]
     conda:
         "envs/sbx_coverage.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-coverage"
     shell:
         """
         samtools sort -@ {threads} -o {output} {input} 2>&1 | tee {log}
@@ -83,6 +99,8 @@ rule mapping_depth:
         LOG_FP / "mapping_depth_{sample}.log",
     conda:
         "envs/sbx_coverage.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-coverage"
     shell:
         """
         samtools depth -aa {input} 1> {output} 2> {log}
@@ -100,6 +118,8 @@ rule get_coverage:
         LOG_FP / "get_coverage_{sample}.log",
     conda:
         "envs/sbx_coverage.yml"
+    container:
+        f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-coverage"
     script:
         "scripts/get_coverage.py"