From 820a188939e418079cb24cf1ac16393d8d70419d Mon Sep 17 00:00:00 2001
From: Alex Lubbock <alex.lubbock@rfi.ac.uk>
Date: Wed, 2 Oct 2024 19:54:14 +0100
Subject: [PATCH] feat: BLAST Dockerfile and GitHub CI pipeline

---
 .github/workflows/build-and-push.yml | 57 ++++++++++++++++++++++++++++
 Dockerfile                           | 13 +++++++
 README.md                            |  5 +++
 3 files changed, 75 insertions(+)
 create mode 100644 .github/workflows/build-and-push.yml
 create mode 100644 Dockerfile
 create mode 100644 README.md

diff --git a/.github/workflows/build-and-push.yml b/.github/workflows/build-and-push.yml
new file mode 100644
index 0000000..4fecae6
--- /dev/null
+++ b/.github/workflows/build-and-push.yml
@@ -0,0 +1,57 @@
+name: Build BLAST container push to quay.io
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Source
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Quay.io
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: rosalindfranklininstitute+github_blast
+          password: ${{ secrets.QUAYIO_TOKEN }}
+
+      - name: Set BLAST version
+        run: |
+          echo BLAST_VERSION=$([ "$GITHUB_REF_TYPE" = "tag" ] && echo $GITHUB_REF_NAME || curl https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/VERSION 2>/dev/null) >> $GITHUB_ENV
+
+      - name: Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            quay.io/rosalindfranklininstitute/blast
+          tags: |
+            type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+          labels: |
+            blast-version=${{ env.BLAST_VERSION }}
+
+      - name: Build and push image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          build-args: |
+            BLAST_VERSION=${{ env.BLAST_VERSION }}
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..e6420c2
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,13 @@
+FROM python:3.12-slim-bookworm AS blast
+
+ARG BLAST_VERSION
+
+RUN apt update && apt install -y wget g++ make liblmdb-dev libsqlite3-dev
+RUN mkdir /blast
+RUN wget -qO- https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-src.tar.gz \
+    | tar xz --strip-components 2 -C /blast
+WORKDIR /blast
+RUN ./configure --with-projects=scripts/projects/blast/project.lst
+RUN cd ReleaseMT/build && make all_p
+
+ENV PATH="$PATH:/blast/ReleaseMT/bin"
\ No newline at end of file
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..a5524d5
--- /dev/null
+++ b/README.md
@@ -0,0 +1,5 @@
+# NCBI Blast+ tools
+
+Containerised build of [BLAST+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html).
+
+Work in progress!
\ No newline at end of file