Merge pull request #6 from Sage-Bionetworks-Workflows/dsl2

Merge  DSL2 into main

.github/workflows/ci.yml

@@ -0,0 +1,45 @@
+name: ci
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'dsl2'
+    paths:
+     - 'docker/**'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v2
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Login to quay.io
+        uses: docker/login-action@v1
+        with:
+          registry: quay.io
+          username: adamjtaylor
+          password: ${{ secrets.QUAY_PASSWORD }}
+      -
+        name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: ./docker
+          push: true
+          tags: |
+            adamjtaylor/htan-artist:latest
+            quay.io/adamjtaylor/htan-artist:latest

.gitignore

@@ -1,4 +1,6 @@
 .nextflow/
 work/
 .nextflow.log*
-test-outputs/
+test-outputs/
+flowchart*
+outputs/*

data/test.csv

@@ -0,0 +1,2 @@
+image,he
+data/cycif_tonsil_very_small.ome.tiff, false

docker/Dockerfile

@@ -5,7 +5,7 @@
 FROM continuumio/miniconda3 AS build
 
 # File Author / Maintainer
-MAINTAINER Adam Taylor <[email protected]>
+LABEL maintainer="Adam Taylor <[email protected]>"
 
 # Install the package as normal:
 COPY environment.yml .
@@ -48,15 +48,20 @@ RUN apt-get update && apt-get install --yes --no-install-recommends \
     libblosc1
 
 RUN source /venv/bin/activate && \
-    git clone https://github.com/adamjtaylor/miniature.git && \
-    git clone https://github.com/jmuhlich/auto-minerva.git && \
-    git clone https://github.com/labsyspharm/minerva-author.git && \
+    #git clone https://github.com/adamjtaylor/miniature.git && \
+    git clone https://github.com/adamjtaylor/miniature.git -b v2 && \
+    #git clone https://github.com/jmuhlich/auto-minerva.git && \
+    git clone https://github.com/adamjtaylor/auto-minerva.git -b minerva1point5 && \
+    git clone https://github.com/labsyspharm/minerva-author.git minerva-author-dev && \
+    git clone https://github.com/labsyspharm/minerva-author.git -b v1.11.2 &&  \
     git clone https://github.com/ncihtan/image-header-validation && \
     wget https://gist.githubusercontent.com/adamjtaylor/964e206bf1e6f302f6e512082e953193/raw/0acdea0736a027a260a0bb598f619552ff106758/index.html && \
     pip install git+https://github.com/labsyspharm/minerva-lib-python@master#egg=minerva-lib && \
     pip install openslide-python && \
     pip install opencv-python-headless \
-    pip install synapseclient
+    pip install synapseclient \
+    pip install mantel \
+    pip install ome_types
 
 ENV VIRTUAL_ENV=/venv
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"

docker/environment.yml

@@ -5,7 +5,7 @@ channels:
   - fastai
   - bioconda
 dependencies:
-  - numpy
+  - numpy=1.23.0
   - Pillow
   - flask
   - waitress
@@ -27,5 +27,8 @@ dependencies:
   - h5py
   - bioformats2raw=0.4.0
   - raw2ometiff
-  - ome-types
   - pip
+  - imagemagick
+  - tiffslide
+  - libvips
+  - estimagic