make ultraplex standalone container for testing

.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"

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

env/demux.yml

@@ -4,5 +4,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - python>3.7
+  - python>3.5
   - pip

env/ultraplex.Dockerfile

@@ -0,0 +1,12 @@
+FROM continuumio/miniconda
+LABEL Sam Widmayer <[email protected]>
+
+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

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