Merge branch 'lipid_dev_wdl' into 'lipid_dev'

Add lipid workflow to lipid_dev branch

See merge request mass-spectrometry/metams!12

.gitignore

@@ -35,4 +35,10 @@ wheels/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
-*.egg
+*.egg
+
+# Raw thermo data
+*.raw
+
+# Metabref token
+*.token

Dockerfile

@@ -21,5 +21,12 @@ COPY metaMS/ /metams/metaMS/
 COPY README.md disclaimer.txt Makefile requirements.txt setup.py /metams/
 COPY db/ /metams/db/
 
+#TODO KRH: Remove this section once the CoreMS package is available on PyPI and installable via the requirements.txt file
+# Copy the CoreMS tar.gz file into the Docker image
+COPY CoreMS-3.2.0.tar.gz /metams/
+
+# Install the CoreMS package from the tar.gz file
+RUN pip install /metams/CoreMS-3.2.0.tar.gz
+
 # Install the MetaMS package in editable mode
 RUN pip3 install --editable .

Dockerfile_test.txt

@@ -0,0 +1,26 @@
+FROM jcarr87/corems-base-py3.10
+
+# set environment variables
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONNET_RUNTIME=coreclr
+
+# set working directory
+WORKDIR /metams
+
+# Set up the directory structure
+COPY metaMS/ /metams/metaMS/
+COPY README.md disclaimer.txt Makefile requirements.txt setup.py /metams/
+COPY db/ /metams/db/
+
+# install dependencies
+RUN pip install --upgrade pip
+RUN apt-get update && apt-get install -y libgomp1
+
+# Install the requirements
+#RUN pip install pythonnet
+RUN pip install -r requirements.txt
+
+# Install the MetaMS package in editable mode
+RUN pip install --editable .
+

Makefile

@@ -73,13 +73,23 @@ docker-build:
 
 	docker build -t microbiomedata/metams:latest .
 
+docker-build-local:
+	docker build -t local-metams:latest .
+
 docker-run:
 	@echo $(data_dir)
 	@echo $(config_dir)
 	@docker run -v $(data_dir):/metams/data -v $(config_dir):/metams/configuration microbiomedata/metams:latest metaMS run-gcms-workflow /metams/configuration/metams.toml
 
-wdl-run :
-	 miniwdl run wdl/metaMS.wdl -i wdl/metams_input.json --verbose --no-cache --copy-input-files
+wdl-run-gcms :
+
+	 miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files
+
+wdl-run-lipid :
+#TODO KRH: remove the docker-build-local when the docker image is available in dockerhub and
+# update the docker image in the wdl file.  Good to rebuild for each run while in development
+	 make docker-build-local
+	 miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
 
 convert_lipid_rst_to_md:
     # convert the lipid documentation from rst to md