Unified Wrapper

.github/workflows/quay-on-tag.yml

@@ -0,0 +1,50 @@
+name: Build & Push Docker image on tag creation
+on:
+    push:
+        tags:
+            - '*'
+
+concurrency:
+    group: docker-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    docker:
+        runs-on: ubuntu-latest
+        permissions:
+            contents: read
+
+        steps:
+            - name: Checkout repository
+              uses: actions/checkout@v4
+
+            - name: Login to Quay
+              uses: docker/login-action@v3
+              with:
+                registry: quay.io
+                username: ${{ secrets.QUAY_USERNAME }}
+                password: ${{ secrets.QUAY_PASSWORD }}
+
+            - name: Docker metadata
+              id: meta
+              uses: docker/metadata-action@v5
+              with:
+                images: quay.io/cellgeni/starsolo
+                tags: |
+                    type=ref,event=tag
+                    # push "latest" only for tags WITHOUT hyphens (excludes pre-releases like v1.0-beta):
+                    type=raw,value=latest,enable=${{ !contains(github.ref_name, '-') }}
+
+            - name: Build and push Docker image
+              uses: docker/build-push-action@v6
+              with:
+                context: .
+                file: Dockerfile
+                push: true
+                tags: ${{ steps.meta.outputs.tags }}
+                labels: ${{ steps.meta.outputs.labels }}
+                cache-from: |
+                    type=registry,ref=quay.io/cellgeni/starsolo:cache
+                    type=gha
+                cache-to: type=registry,ref=quay.io/cellgeni/starsolo:cache,mode=max
+

.github/workflows/test.yml

@@ -0,0 +1,57 @@
+name: "Test Workflow"
+on:
+    push:
+        branches: [main, dev]
+        paths-ignore:
+            - 'data/whitelists.tar.gz'
+            - 'README.md'
+            - 'LICENSE'
+            - 'scripts/**'
+            - 'Dockerfile'
+    pull_request:
+        branches: [main, dev]
+
+jobs:
+    test:
+        runs-on: ubuntu-latest
+        container: quay.io/cellgeni/starsolo:base
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - technology: 10x
+                    - technology: dropseq
+                    - technology: indrops
+                    - technology: smartseq
+                    - technology: rhapsody
+                    - technology: strt
+        name: "Run tests for ${{ matrix.technology }}"
+
+        steps:
+            - name: Checkout repository
+              uses: actions/checkout@v4
+
+            - name: Unpack test data
+              run: tar -xzf data/test.tar.gz
+
+            - name: Run tests
+              run: |
+                set -e
+                technology=${{ matrix.technology }}
+                if [ "$technology" = "smartseq" ]; then
+                    bin/starsolo smartseq \
+                        data/test/fastqs/smartseq/smartseq_example.manifest.tsv \
+                        --ref data/test/reference/index \
+                        --no-bam \
+                        --cpus 1
+                else
+                    bin/starsolo $technology \
+                        data/test/fastqs/${technology} \
+                        "$technology" \
+                        --ref data/test/reference/index \
+                        --whitelist-dir data/test/whitelists \
+                        --no-bam \
+                        --cpus 1
+                fi
+
+

Dockerfile

@@ -3,14 +3,14 @@ FROM ubuntu:20.04
 ENV DEBIAN_FRONTEND=noninteractive
 
 ARG star_version=2.7.10a_alpha_220818
-ARG samtools_version=1.15.1
+ARG samtools_version=1.21
 ARG bbmap_version=38.97
-ARG rsem_version=1.3.3
+ARG seqtk_version=1.4
 
 #Install OS packages
 RUN apt-get update && apt-get -y --no-install-recommends -qq install \
     wget gcc build-essential software-properties-common libz-dev \
-    git libncurses5-dev libbz2-dev liblzma-dev default-jre bsdmainutils
+    git libncurses5-dev libbz2-dev liblzma-dev default-jre bsdmainutils pbzip2
 
 #Install STAR
 RUN wget --no-check-certificate https://github.com/alexdobin/STAR/archive/${star_version}.tar.gz && \
@@ -20,10 +20,11 @@ RUN wget --no-check-certificate https://github.com/alexdobin/STAR/archive/${star
     cd / && rm ${star_version}.tar.gz 
 
 #Install seqtk
-RUN git clone https://github.com/lh3/seqtk.git && \
-    mv seqtk /opt && \
-    cd /opt/seqtk && \
-    make
+RUN wget --no-check-certificate https://github.com/lh3/seqtk/archive/refs/tags/v${seqtk_version}.tar.gz && \
+    tar -xzf v${seqtk_version}.tar.gz -C /opt && \
+    cd /opt/seqtk-${seqtk_version} && \
+    make && \
+    cd / && rm v${seqtk_version}.tar.gz
 
 #Install samtools
 RUN wget https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2 && \
@@ -41,19 +42,29 @@ RUN wget https://sourceforge.net/projects/bbmap/files/BBMap_${bbmap_version}.tar
     ./stats.sh in=resources/phix174_ill.ref.fa.gz && \
     cd / && rm BBMap_${bbmap_version}.tar.gz
 
-#Install RSEM
-RUN wget https://github.com/deweylab/RSEM/archive/refs/tags/v${rsem_version}.tar.gz && \
-    tar -xzf v${rsem_version}.tar.gz -C /opt && \
-    cd /opt/RSEM-${rsem_version} && \
-    make && \
-    cd / && rm v${rsem_version}.tar.gz
+# Install this repository
+COPY . /opt/STARsolo
+RUN cd /opt/STARsolo &&\
+    rm data/test.tar.gz &&\
+    tar -xzf data/whitelists.tar.gz &&\
+    ./install.sh
 
-ENV PATH="${PATH}:/opt/STAR-${star_version}/source:/opt/seqtk:/opt/bbmap:/opt/RSEM-${rsem_version}"     
+# Set PATH to include all binaries
+ENV STARSOLO_WL_DIR=/opt/STARsolo/data/whitelists
+ENV PATH="/opt/STARsolo/bin:${PATH}:/opt/STAR-${star_version}/source:/opt/seqtk-${seqtk_version}:/opt/bbmap"     
 
 #Saving Software Versions to a file
 RUN echo "STAR version: ${star_version}" >> versions.txt && \
     echo "samtools version: ${samtools_version}" >> versions.txt && \
     echo "BBMap version: ${bbmap_version}" >> versions.txt && \
-    echo "RSEM version: ${rsem_version}" >> versions.txt && \
-    seqtk_version=`strings $(which seqtk) | grep 'Version:' | cut -f 2 -d " "` && \
     echo "seqtk version: ${seqtk_version}" >> versions.txt 
+
+COPY Dockerfile /docker/
+RUN chmod -R 755 /docker
+
+
+
+# Default entrypoint: run the CLI
+WORKDIR /workdir
+ENTRYPOINT ["starsolo"]
+CMD ["--help"]