From 3a24facd062afc040296822871276344d13ab048 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Mon, 11 Dec 2023 15:16:25 -0700
Subject: [PATCH] adding pango-collapse

---
 .github/workflows/update_pango-collapse.yml | 69 +++++++++++++++++++++
 pango-collapse/Dockerfile                   | 37 +++++++++++
 2 files changed, 106 insertions(+)
 create mode 100644 .github/workflows/update_pango-collapse.yml
 create mode 100644 pango-collapse/Dockerfile

diff --git a/.github/workflows/update_pango-collapse.yml b/.github/workflows/update_pango-collapse.yml
new file mode 100644
index 0000000..f107721
--- /dev/null
+++ b/.github/workflows/update_pango-collapse.yml
@@ -0,0 +1,69 @@
+name: Update pango-collapse
+
+on: 
+  workflow_dispatch:
+  schedule:
+    - cron: '30 5 * * TUE'
+
+run-name: Updating pango-collapse
+
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get latest release
+        uses: rez0n/actions-github-release@main
+        id: latest_release
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          repository: MDU-PHL/pango-collapse
+          type: "stable"
+          
+      - uses: actions/checkout@v3
+     
+      - name: Remove V
+        id: strip
+        run: |
+          version=$(echo "${{ steps.latest_release.outputs.release }}" | sed 's/V//g' | sed 's/v//g' )
+          echo "The version is $version"
+          echo "version=$version" >> $GITHUB_OUTPUT
+
+      - name: pull repo
+        uses: actions/checkout@v3
+
+      - name: Get current date
+        id: date
+        run: |
+          date=$(date '+%Y-%m-%d')
+          echo "the date is $date"
+          echo "date=$date" >> $GITHUB_OUTPUT
+          
+      - name: check paths
+        run: ls && ls ./pango-collapse
+        
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to Quay
+        uses: docker/login-action@v2
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_PASSWORD }}
+
+      - name: Build and push to Quay
+        uses: docker/build-push-action@v3
+        with:
+          file: ./pango-collapse/Dockerfile
+          build-args: VER=${{ steps.strip.outputs.version }}
+          push: true
+          tags: quay.io/uphl/pango-collapse:${{ steps.strip.outputs.version }}-${{ steps.date.outputs.date }}
+
+      - name: Build and push latest tag to Quay
+        uses: docker/build-push-action@v3
+        with:
+          file: ./pango-collapse/Dockerfile
+          build-args: VER=${{ steps.strip.outputs.version }}
+          push: true
+          tags: quay.io/uphl/pango-collapse:latest   
diff --git a/pango-collapse/Dockerfile b/pango-collapse/Dockerfile
new file mode 100644
index 0000000..2ffade3
--- /dev/null
+++ b/pango-collapse/Dockerfile
@@ -0,0 +1,37 @@
+FROM python:3.9.17-slim as app
+
+# List all software versions are ARGs near the top of the dockerfile
+# 'ARG' sets environment variables during the build stage
+# ARG variables are ONLY available during image build, they do not persist in the final image
+ARG VER="0.7.2"
+
+# 'LABEL' instructions tag the image with metadata that might be important to the user
+LABEL base.image="python:3.9.17-slim"
+LABEL dockerfile.version="1"
+LABEL software="pango-collapse"
+LABEL software.version="${VER}"
+LABEL description="collapse lineages up to the first user defined parent lineage"
+LABEL website="https://github.com/MDU-PHL/pango-collapse"
+LABEL license="https://github.com/MDU-PHL/pango-collapse?tab=GPL-3.0-1-ov-file#readme"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+# 'RUN' executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    procps \
+    ca-certificates && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Install and/or setup more things. Make /data for use as a working dir
+# For readability, limit one install per 'RUN' statement.
+RUN pip install --no-cache pango-collapse==${VER} && pango-collapse --help 
+
+ENV PATH="$PATH" \
+    LC_ALL=C
+
+# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
+CMD pango-collapse --help 
+
+# 'WORKDIR' sets working directory
+WORKDIR /data