Bmdrc pipeline

.github/workflows/docker.yml

@@ -18,14 +18,25 @@ on:
 
 
 jobs:
-  build-and-push-sample:
+  # setup:
+  #   runs-on: ubuntu-latest
+  #   outputs:
+  #     docker_username: ${{ secrets.DOCKERHUB_USERNAME }}
+  #     docker_password: ${{ secrets.DOCKERHUB_PASSWORD }}
+  #   steps:
+
+
+  build-push-sample:
+    # needs: setup
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v3
       - name: Set up Docker Buildx
+        id: buildx
         uses: docker/setup-buildx-action@v3
       - name: Login to DockerHub
+        id: login
         uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -34,18 +45,21 @@ jobs:
         uses: docker/build-push-action@v3
         with:
          file: sampleChemMapping/Dockerfile
-         tags: sgosline/srp-samplechem:latest
          platforms: linux/amd64,linux/arm64
          push: true
+         tags: sgosline/srp-samplechem:latest
 
   build-push-expo:
+    # needs: setup
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      - name: Set up Docker Buildx     
+      - name: Set up Docker Buildx
+        id: buildx
         uses: docker/setup-buildx-action@v3
       - name: Login to DockerHub
+        id: login
         uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -55,17 +69,20 @@ jobs:
         with:
          file: exposome/Dockerfile
          platforms: linux/amd64,linux/arm64
-         tags: sgosline/srp-exposome:latest
          push: true
+         tags: sgosline/srp-exposome:latest
 
   build-push-exp:
+    # needs: setup
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v3
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3     
+        id: buildx
+        uses: docker/setup-buildx-action@v3
       - name: Login to DockerHub
+        id: login
         uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
@@ -74,16 +91,33 @@ jobs:
         uses: docker/build-push-action@v3
         with:
          file: zfExp/Dockerfile
+         platforms: linux/amd64,linux/arm64
          push: true
+         tags: sgosline/srp-zfexp:latest
+
+  build-push-bmdrc:
+    # needs: setup
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to DockerHub
+        id: login
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Build and push bmd
+        uses: docker/build-push-action@v3
+        with:
+         file: zfBmd/Dockerfile
          platforms: linux/amd64,linux/arm64
-         tags: sgosline/srp-zfexp
-#      - name: Build and push bmd
-#        uses: docker/build-push-action@v6
-#        with:
-#          context: zfBmd
-#          push: true
-#          tags: sgosline/srp-zfbmd:latest
-#          platforms: linux/amd64,linux/arm64       
+         push: true
+         tags: sgosline/srp-zfbmd:latest
+
 #      - name: Build and push bmd2Samps
 #        uses: docker/build-push-action@v6
 #        with:

.gitignore

@@ -58,3 +58,8 @@ tmp/
 new_*
 Reformatted*
 .vscode
+zfBmd/files/
+new_BMDS_BC.csv
+new_Dose_BC.csv
+new_Fits_BC.csv
+new_report_BC/*

exposome/Dockerfile

@@ -28,4 +28,4 @@ RUN pip3 install -r requirements.txt
 # RUN Rscript -e "install.packages(c('jsonlite','dplyr','httr','tidyr'), dependencies=TRUE,repos='http://cran.rstudio.com')"
 
 
-ENTRYPOINT ["python","/app/build_script.py","--expo"]
+ENTRYPOINT ["python", "/app/build_script.py", "--expo"]

exposome/README.md

@@ -1,20 +1,25 @@
-## Exposome data processing
+## Exposome Data Processing
+
 This module contains the scripts and docker image to build the
 exposome data.
 
+To test locally, you can run this script:
 
-To test locally you can run this script:
-```
+```bash
 python build_script.py --expo
 
 ```
 
 To test with all the R/Python requirements already installed, use the
 docker image:
 
-```
+```bash
 docker build . -t srp-exposome -f exposome/Dockerfile
-docker run -v $PWD:/tmp srp-exposome
+docker run -v $PWD/tmp:/tmp srp-exposome
 ```
 
-
+By default, this writes all output files to a `tmp` directory inside the current working directory from which the container is run. You can change this directory to point to anywhere you want output files to be written:
+
+```bash
+docker run -v /path/to/output_dir:/tmp srp-exposome --output_dir /tmp
+```

sampleChemMapping/Dockerfile

@@ -6,8 +6,6 @@ RUN apt-get install -y --allow-unauthenticated --fix-missing  python3-pip python
 # r-base gcc-12 build-essential libpq-dev python3-venv libxml2-dev libcurl4-openssl-dev
 
 RUN python3 -m venv /opt/venv
-
-
 ENV PATH="/opt/venv/bin:$PATH"
 WORKDIR /app
 
@@ -22,5 +20,5 @@ COPY requirements.txt .
 RUN pip3 install --upgrade pip
 RUN pip3 install -r requirements.txt
 
-ENTRYPOINT ["python","/app/build_script.py","--samps"]
+ENTRYPOINT ["python", "/app/build_script.py", "--samps"]
 

sampleChemMapping/README.md

@@ -1,27 +1,31 @@
 ## BMD to Sample mapping
 
-This module consumes bench mark dose measurements from the pipeline and maps them to specific chemical metadata and concentrations in sample extracts. 
+This module consumes bench mark dose measurements from the pipeline and maps them to specific chemical metadata and concentrations in sample extracts.
 
-To run/test in this repo:
-```
-Rscript sampleChemMapping/mapSamplesToChems.R --sampId="+smap+' --chemId='+cid+\
-            ' --epMap='+emap+' --chemClass='+cclass+\
-            ' --compToxFile='+ctfile+' --sampleFiles='+fses+' --chemDesc='+desfile+\
-            ' --sampMap='+smap
+To run/test in this repo, navigate to the root of the repo and run:
+
+```bash
+python build_script.py --samps
 ```
 
 To run/test docker image (from root of repo):
 
-```
+```bash
 docker build . -t srp-samplechem -f sampleChemMapping/Dockerfile
-docker run -v $PWD:/tmp srp-samplechem
+docker run -v $PWD/tmp:/tmp srp-samplechem --output_dir /tmp
+```
+
+By default, this writes all output files to a `tmp` directory inside the current working directory from which the container is run. You can change this directory to point to anywhere you want output files to be written:
+
+```bash
+docker run -v /path/to/output_dir:/tmp srp-samplechem --output_dir /tmp
 ```
 
 ### Chemical identifiers
 
-All chemicals must have a `cas_number` that has data download from the [EPA Comptox website](https://comptox.epa.gov/dashboard/batch-search). 
+All chemicals must have a `cas_number` that has data download from the [EPA Comptox website](https://comptox.epa.gov/dashboard/batch-search).
 
-All cas numbers must have a `Chemical_ID` - these either come from the Tanguay lab or are generated manually by us. Either way they are stored in [./data/chemicalIdMapping.csv](data/chemicalIdMapping.csv). 
+All cas numbers must have a `Chemical_ID` - these either come from the Tanguay lab or are generated manually by us. Either way they are stored in [./data/chemicalIdMapping.csv](data/chemicalIdMapping.csv).
 
 ### Sample measurements
 
@@ -32,4 +36,4 @@ sample mapping file.
 ### Benchmark dose values
 
 These are processed from the stored BMD files and the recalculated
-ones passed into the argument. 
+ones passed into the argument.