Adding rsem 1.2.21 dockerfile

.github/workflows/rsem1.2.21docker-publish.yml

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+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  #schedule:
+    #- cron: '37 6 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+    #tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}/tools/rsem
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+     # - name: Install cosign
+       # if: github.event_name != 'pull_request'
+     #  uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
+       # with:
+       #   cosign-release: 'v1.7.1'
+
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+
+     # - name: Log into registry Docker hub
+        #if: github.event_name != 'pull_request'
+       # uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+      #  with:
+       #   username: ${{ secrets.DOCKERHUB_USERNAME }}
+       #   password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Log in to the Container registry 
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: 
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+            #docker.io/reddylab/rsem
+          tags: latest
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: ./tools/rsem/1.2.21/
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/star-utils.yml

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+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation
+
+on:
+  #schedule:
+   # - cron: '43 13 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+   # tags: [ v*.*.*]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+ REGISTRY: ghcr.io
+
+  # github.repository as <account>/<repo>
+ IMAGE_NAME: 
+      ${{ github.repository }}/tools/star-utils   
+
+jobs:
+  build:
+
+    name: Push Docker image to multiple registries
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      #- name: Install cosign
+        #if: github.event_name != 'pull_request'
+       # uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
+       # with:
+       #   cosign-release: 'v1.7.1'
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+     # - name: Log into Docker hub 
+        #if: github.event_name != 'pull_request'
+        #uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        #with:
+       #   username: ${{ secrets.DOCKER_USERNAME }}
+        #  password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Log in to the Container registry  
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: |
+              ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}  
+          tags: latest    
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: ./tools/star-utils/
+          #push: ${{ github.event_name != 'pull_request' }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/windowtrimmer.yml

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+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  #schedule:
+   # - cron: '15 23 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+    #tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}/tools/windowtrimmer
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      #- name: Install cosign
+       # if: github.event_name != 'pull_request'
+        #uses: sigstore/cosign-installer@d6a3abf1bdea83574e28d40543793018b6035605
+        #with:
+         # cosign-release: 'v1.7.1'
+
+
+      # Workaround: https://github.com/docker/build-push-action/issues/461
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      # - name: Log into Docker hub 
+        #if: github.event_name != 'pull_request'
+        #uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        #with:
+       #   username: ${{ secrets.DOCKER_USERNAME }}
+        #  password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Log in to the Container registry  
+        #if: github.event_name != 'pull_request'
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: latest
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        with:
+          context: ./tools/windowtrimmer/
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      #- name: Sign the published Docker image
+      #  if: ${{ github.event_name != 'pull_request' }}
+      #  env:
+      #    COSIGN_EXPERIMENTAL: "true"
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+      #  run: cosign sign ${{ steps.meta.outputs.tags }}@${{ steps.build-and-push.outputs.digest }}

tools/rsem/1.2.21/Dockerfile

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+FROM phusion/baseimage:focal-1.2.0
+MAINTAINER Alejandro Barrera <alejandro.barrera@duke.edu>
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+  build-essential \
+  g++ \
+  zlib1g-dev \
+  libncurses-dev \
+  curl \
+  unzip
+
+#########################################################
+# NOTE: Added here Bowtie image given that CWL          #
+# ^^^^  will not allow multiple Docker dependencies     #
+#       at this point.                                  #
+#########################################################
+# Installs bowtie from compiled distribution into /opt/bowtie
+ENV BOWTIE_URL=http://sourceforge.net/projects/bowtie-bio/files/bowtie
+ENV BOWTIE_RELEASE=0.12.9
+ENV DEST_DIR=/opt
+
+# Download Bowtie, unzip it and remove .zip file
+RUN curl -SLo ${DEST_DIR}/bowtie-${BOWTIE_RELEASE}.zip ${BOWTIE_URL}/${BOWTIE_RELEASE}/bowtie-${BOWTIE_RELEASE}-linux-x86_64.zip/download && unzip ${DEST_DIR}/bowtie-${BOWTIE_RELEASE}.zip -d ${DEST_DIR} && rm ${DEST_DIR}/bowtie-${BOWTIE_RELEASE}.zip
+
+# Add bowtie path to the enviroment
+ENV PATH=${DEST_DIR}/bowtie-${BOWTIE_RELEASE}:$PATH
+
+# Define ENV variables for download
+ENV RSEM_RELEASE=1.2.21
+ENV RSEM_URL=https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_RELEASE}.tar.gz
+#ENV RSEM_URL=https://github.com/deweylab/RSEM/releases/tag/v${RSEM_RELEASE}.tar.gz
+ENV DEST_DIR=/opt
+
+# Download and unpack RSEM sources, make & install and remove unnecessary files
+RUN curl -SLo ${DEST_DIR}/RSEM-${RSEM_RELEASE}.tar.gz ${RSEM_URL} && \
+    tar xzvf ${DEST_DIR}/RSEM-${RSEM_RELEASE}.tar.gz -C ${DEST_DIR} && \
+    cd ${DEST_DIR}/RSEM-${RSEM_RELEASE} && \
+    sed -i.bak "s/CC = g++/CC = g++ -std=gnu++98/" Makefile && \
+    make && \
+    rm -rf ${DEST_DIR}/RSEM-${RSEM_RELEASE}.tar.gz
+
+# Add RSEM path to ENV path
+ENV PATH=${DEST_DIR}/RSEM-${RSEM_RELEASE}/:$PATH
+
+# List executables provided by rsem
+
+CMD ["find", "/opt/", "-executable", "-type", "f", "-iname", "rsem*"]

tools/star-utils/Dockerfile

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+FROM python:2.7
+MAINTAINER alejandro.barrera@duke.edu
+
+ADD src /src
+WORKDIR /src
+
+RUN pip install -r /src/requirements.txt
+
+RUN chmod +x /src/create_SJ.out.tab.Pass1.conservative.sjdb.py
+ENV PATH /src/:$PATH
+CMD ["create_SJ.out.tab.Pass1.conservative.sjdb.py"]