diff --git a/.github/workflows/build_ultraplex_docker.yml b/.github/workflows/build_ultraplex_docker.yml new file mode 100644 index 0000000..15cbc40 --- /dev/null +++ b/.github/workflows/build_ultraplex_docker.yml @@ -0,0 +1,29 @@ +name: Build ultraplex container (env/ultraplex.Dockerfile) + +on: + push: + paths: + - 'env/ultraplex.Dockerfile' + - '.github/workflows/build_ultraplex_docker.yml' + pull_request: + paths: + - 'env/ultraplex.Dockerfile' + - '.github/workflows/build_ultraplex_docker.yml' + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + + # Build Tools + - name: Build and Publish + uses: elgohr/Publish-Docker-Github-Action@v5 + with: + name: sjwidmay/stitch_nf + username: ${{ secrets.SJW_DOCKER_USER }} + password: ${{ secrets.SJW_DOCKER_PASS }} + snapshot: true + dockerfile: ultraplex.Dockerfile + workdir: "env" + tags: "ultraplex" \ No newline at end of file diff --git a/env/demux.Dockerfile b/env/demux.Dockerfile index f9bb3ae..761ebc1 100644 --- a/env/demux.Dockerfile +++ b/env/demux.Dockerfile @@ -10,4 +10,3 @@ RUN apt-get --allow-releaseinfo-change update \ && apt-get install -y g++ RUN pip install demultiplex -RUN pip install ultraplex diff --git a/env/demux.yml b/env/demux.yml index 380d70c..fcfcf62 100644 --- a/env/demux.yml +++ b/env/demux.yml @@ -4,5 +4,5 @@ channels: - bioconda - conda-forge dependencies: - - python>3.7 + - python>3.5 - pip diff --git a/env/ultraplex.Dockerfile b/env/ultraplex.Dockerfile new file mode 100644 index 0000000..dcccd54 --- /dev/null +++ b/env/ultraplex.Dockerfile @@ -0,0 +1,12 @@ +FROM continuumio/miniconda +LABEL Sam Widmayer + +COPY ultraplex.yml . +RUN \ + conda env update -n root -f ultraplex.yml \ +&& conda clean -a + +RUN apt-get --allow-releaseinfo-change update \ + && apt-get install -y g++ + +RUN pip install ultraplex \ No newline at end of file diff --git a/env/ultraplex.yml b/env/ultraplex.yml new file mode 100644 index 0000000..67d0ff9 --- /dev/null +++ b/env/ultraplex.yml @@ -0,0 +1,36 @@ +name: ultraplex +channels: + - conda-forge + - bioconda + - r + - bcbio + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=1_gnu + - ca-certificates=2021.1.19=h06a4308_0 + - certifi=2020.12.5=py36h5fab9bb_1 + - dataclasses=0.7=pyhe4b4509_6 + - dnaio=0.5.0=py36h4c5857e_0 + - isa-l=2.30.0=ha770c72_2 + - ld_impl_linux-64=2.35.1=hea4e1c9_2 + - libffi=3.3=h58526e2_2 + - libgcc-ng=9.3.0=h2828fa1_18 + - libgomp=9.3.0=h2828fa1_18 + - libstdcxx-ng=9.3.0=h6de172a_18 + - ncurses=6.2=h58526e2_4 + - openssl=1.1.1j=h7f98852_0 + - pigz=2.5=h27826a3_0 + - pip=21.0.1=pyhd8ed1ab_0 + - python=3.6.13=hffdb5ce_0_cpython + - python-isal=0.5.0=py36h8f6f2f9_0 + - python_abi=3.6=1_cp36m + - readline=8.1=h27cfd23_0 + - setuptools=52.0.0=py36h06a4308_0 + - sqlite=3.34.0=h74cdb3f_0 + - tk=8.6.10=h21135ba_1 + - ultraplex=1.1.3=py36h4c5857e_0 + - wheel=0.36.2=pyhd3deb0d_0 + - xopen=1.1.0=py36h5fab9bb_1 + - xz=5.2.5=h516909a_1 + - zlib=1.2.11=h516909a_1010 \ No newline at end of file