Merge pull request #2 from kapsakcj/add-docker

added Dockerfile and updated main README.md

.github/workflows/linux-cpp.yml

@@ -29,3 +29,20 @@ jobs:
             ./*
             test/* 
         retention-days: 14
+
+  build-docker:
+
+      runs-on: ubuntu-latest
+
+      steps:
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build to test
+        uses: docker/build-push-action@v5
+        with:
+          push: false
+

Dockerfile

@@ -0,0 +1,39 @@
+FROM ubuntu:jammy
+
+LABEL base.image="ubuntu:jammy"
+LABEL software="stxtyper"
+LABEL description="Scan contig files against PubMLST typing schemes"
+LABEL website="https://github.com/evolarjun/stxtyper"
+LABEL license="https://github.com/evolarjun/stxtyper/blob/main/LICENSE"
+LABEL maintainer="Curtis Kapsak"
+LABEL maintainer.email="kapsakcj@gmail.com"
+
+# install dependencies via apt; cleanup apt garbage
+# blast from ubuntu:jammy is v2.12.0 (as of 2024-03-26)
+# procps is for ps command (required for nextflow)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ wget \
+ ca-certificates \
+ make \ 
+ g++ \
+ ncbi-blast+ \
+ procps && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# bring in stxtyper code
+COPY . /stxtyper
+
+# compile 
+# run test script
+# TODO in future: move executables to /usr/local/bin and delete source code (for smaller image) 
+RUN cd /stxtyper && \
+    make && \
+    bash test_stxtyper.sh && \
+    tblastn -help && \
+    ./stxtyper --help
+
+# set PATH to include where stxtyper & fasta_check executables exist
+ENV PATH="${PATH}:/stxtyper" 
+
+# set final working directory as /data for passing data in/out of container
+WORKDIR /data

README.md

@@ -39,6 +39,24 @@ If you install BLAST via conda in this way you will need to run `conda activate
     make
     make test
 
+## Docker
+
+Pre-built docker images are available on [Dockerhub](https://hub.docker.com/r/kapsakcj/stxtyper), though they may not be as up-to-date as the source code. To pull the image from Dockerhub, run:
+
+```bash
+# Pull the latest image
+docker pull kapsakcj/stxtyper:latest
+
+# Optionally, pull from a specific commit hash
+docker pull kapsakcj/stxtyper:<commit_hash>
+```
+
+A Dockerfile is included in the repository. To build the Docker image locally, run this command when in the root directory of the repository:
+
+```bash
+docker build -t stxtyper .
+```
+
 # Usage
 
     stxtyper -n <assembled_nucleotide.fa> [<options>]