From dfff24f0e76ed2d4f3b8dea8e908cab46df7dadf Mon Sep 17 00:00:00 2001
From: chasemc <18691127+chasemc@users.noreply.github.com>
Date: Wed, 24 Jul 2024 11:34:55 -0500
Subject: [PATCH] fix: docker workflow

---
 .github/workflows/docker.yml        | 44 ++++++++++++++---------------
 dockerfiles/prokka/Dockerfile       | 19 -------------
 dockerfiles/prokka/environment.yaml | 11 --------
 3 files changed, 22 insertions(+), 52 deletions(-)
 delete mode 100644 dockerfiles/prokka/Dockerfile
 delete mode 100644 dockerfiles/prokka/environment.yaml

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index fe694ba..648bddd 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -59,25 +59,25 @@ jobs:
         - name: Push Docker images
           run: |
               docker push chasemc2/sgnf-antismash:$RELEASE_NUMBER
-  build_and_push_prokka:
-      name: Build and push prokka
-      runs-on: ubuntu-latest
-      continue-on-error: true
-      steps:
-        - name: Check out the repo
-          uses: actions/checkout@v4
-        - name: Log in to Docker Hub
-          uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
-          with:
-            username: ${{ secrets.DOCKER_USERNAME }}
-            password: ${{ secrets.DOCKERHUBPAT }}
-        - name: Get release number without preceding v
-          id: get_release_number
-          run: echo "RELEASE_NUMBER=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV
-        - name: Build Docker images
-          run: |
-              cd dockerfiles/prokka
-              docker build -t chasemc2/sgnf-prokka:$RELEASE_NUMBER .
-        - name: Push Docker images
-          run: |
-              docker push chasemc2/sgnf-prokka:$RELEASE_NUMBER
+  # build_and_push_prokka:
+  #     name: Build and push prokka
+  #     runs-on: ubuntu-latest
+  #     continue-on-error: true
+  #     steps:
+  #       - name: Check out the repo
+  #         uses: actions/checkout@v4
+  #       - name: Log in to Docker Hub
+  #         uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+  #         with:
+  #           username: ${{ secrets.DOCKER_USERNAME }}
+  #           password: ${{ secrets.DOCKERHUBPAT }}
+  #       - name: Get release number without preceding v
+  #         id: get_release_number
+  #         run: echo "RELEASE_NUMBER=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV
+  #       - name: Build Docker images
+  #         run: |
+  #             cd dockerfiles/prokka
+  #             docker build -t chasemc2/sgnf-prokka:$RELEASE_NUMBER .
+  #       - name: Push Docker images
+  #         run: |
+  #             docker push chasemc2/sgnf-prokka:$RELEASE_NUMBER
diff --git a/dockerfiles/prokka/Dockerfile b/dockerfiles/prokka/Dockerfile
deleted file mode 100644
index 8f27748..0000000
--- a/dockerfiles/prokka/Dockerfile
+++ /dev/null
@@ -1,19 +0,0 @@
-FROM mambaorg/micromamba:1.4.3
-
-COPY environment.yaml /tmp/env.yaml
-
-# Not running clusterblast, etc. So remove as many databases as possible without
-# breaking antismash (don't delete resfams db)
-RUN micromamba install -y -n base -f /tmp/env.yaml && \
-    micromamba clean --all --yes && \
-    find /opt/conda/lib -wholename "**/databases/clusterblast" -prune -type d -exec rm -r "{}" \; && \
-    find /opt/conda/lib -wholename "**/databases/clustercompare" -prune -type d -exec rm -r "{}" \; && \
-    find /opt/conda/lib -wholename "**/databases/pfam" -prune -type d -exec rm -r "{}" \; && \
-    find /opt/conda/lib -wholename "**/databases/tigrfam" -prune -type d -exec rm -r "{}" \;
-
-USER $MAMBA_USER
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-
-
-
-
diff --git a/dockerfiles/prokka/environment.yaml b/dockerfiles/prokka/environment.yaml
deleted file mode 100644
index db4f1de..0000000
--- a/dockerfiles/prokka/environment.yaml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: sgnf-prokka
-
-channels:
-  - anaconda
-  - bioconda
-  - conda-forge
-  - defaults
-
-dependencies:
-  - bioconda::prokka==1.14.6
-  - procps-ng>=4.0 # required by nextflow