added github/actions automated Singularity container build

.github/workflows/singularity.yml

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+name: Singularity Build (native)
+on: 
+  push:
+
+    # Edit the branches here if you want to change deploy behavior
+    branches:
+      - main
+      - master
+
+  # Do the builds on all pull requests (to test them)
+  pull_request: []
+
+jobs:
+  changes:
+    name: "Changed Singularity Recipes"
+    runs-on: ubuntu-latest
+    outputs:
+      changed_file: ${{ steps.files.outputs.added_modified }}
+    steps:
+      - id: files
+        uses: jitterbit/get-changed-files@b17fbb00bdc0c0f63fcf166580804b4d2cdc2a42
+        with:
+          format: 'json'
+
+  build-test-containers:
+    needs:
+      - changes
+    runs-on: ubuntu-latest
+    strategy:
+      # Keep going on other deployments if anything bloops
+      fail-fast: false
+      matrix:
+        changed_file: ${{ fromJson(needs.changes.outputs.changed_file) }}
+
+    name: Check ${{ matrix.changed_file }}
+    steps:
+      - name: Continue if Singularity Recipe
+        run: |
+          # Continue if we have a changed Singularity recipe
+          if [[ "${{ matrix.changed_file }}" = *Singularity* ]]; then
+            echo "keepgoing=true" >> $GITHUB_ENV
+          fi          
+
+      - name: Set up Go 1.13
+        if: ${{ env.keepgoing == 'true' }}
+        uses: actions/setup-go@v1
+        with:
+          go-version: 1.13
+        id: go
+
+      - name: Install Dependencies
+        if: ${{ env.keepgoing == 'true' }}
+        run: |
+          sudo apt-get update && sudo apt-get install -y \
+            build-essential \
+            libssl-dev \
+            uuid-dev \
+            libgpgme11-dev \
+            squashfs-tools \
+            libseccomp-dev \
+            pkg-config
+
+      - name: Install Singularity
+        if: ${{ env.keepgoing == 'true' }}
+        env:
+          SINGULARITY_VERSION: 3.8.1
+          GOPATH: /tmp/go
+
+        run: |
+          mkdir -p $GOPATH
+          sudo mkdir -p /usr/local/var/singularity/mnt && \
+          mkdir -p $GOPATH/src/github.com/sylabs && \
+          cd $GOPATH/src/github.com/sylabs && \
+          wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \
+          tar xzv && \
+          cd singularity-ce-${SINGULARITY_VERSION} && \
+          ./mconfig -p /usr/local && \
+          make -C builddir && \
+          sudo make -C builddir install          
+
+      - name: Check out code for the container build
+        if: ${{ env.keepgoing == 'true' }}
+        uses: actions/checkout@v2
+
+      - name: Build Container
+        if: ${{ env.keepgoing == 'true' }}
+        env:
+          recipe: ${{ matrix.changed_file }}
+        run: |
+         ls 
+         if [ -f "${{ matrix.changed_file }}" ]; then
+            sudo -E singularity build container.sif ${{ matrix.changed_file }}
+            tag=$(echo "${recipe/Singularity\./}")
+            if [ "$tag" == "Singularity" ]; then
+                tag=latest
+            fi
+            # Build the container and name by tag
+            echo "Tag is $tag."
+            echo "tag=$tag" >> $GITHUB_ENV
+         else
+           echo "${{ matrix.changed_file }} is not found."
+           echo "Present working directory: $PWD"
+           ls
+         fi
+
+      - name: Login and Deploy Container
+        if: (github.event_name != 'pull_request')
+        env:
+          keepgoing: ${{ env.keepgoing }}
+        run: |         
+            if [[ "${keepgoing}" == "true" ]]; then
+                echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
+                singularity push container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${tag}
+            fi

Singularity

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+Bootstrap: docker
+From: ubuntu:20.04
+IncludeCmd: yes
+
+%environment
+#R_VERSION=4.1
+#export R_VERSION
+#R_CONFIG_DIR=/etc/R/
+#export R_CONFIG_DIR
+export LC_ALL=C
+export PATH=$PATH:/opt/software/miniconda3/bin
+
+%post
+  apt-get update
+  apt-get install -y apt-transport-https apt-utils software-properties-common
+  apt-get install -y add-apt-key
+  export DEBIAN_FRONTEND=noninteractive
+  ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
+  apt-get install -y tzdata
+  dpkg-reconfigure --frontend noninteractive tzdata
+
+  apt-get install -y wget
+
+  mkdir -p /opt/software
+
+  # MAPseq installation
+  cd /opt/software
+  wget -q https://github.com/jfmrod/MAPseq/releases/download/2.0.1alpha/mapseq-2.0.1alpha-linux.tar.gz
+  tar xvzf mapseq-2.0.1alpha-linux.tar.gz
+  rm mapseq-2.0.1alpha-linux.tar.gz
+  mv mapseq-2.0.1alpha-linux mapseq
+
+  ln -s /opt/software/mapseq/mapseq /usr/bin/
+  ln -s /opt/softwaremapseq/share /usr/bin/