Manuscript update (#17)

* unit tests with sample data

* update readme with conda and docker installation

* fix error with singleton clusters

Author: jonperdomo

.github/workflows/build-tests.yml

@@ -17,11 +17,11 @@ jobs:
       with:
         repo: 'WGLab/ContextSV'
         version: 'tags/v0.1.0'
-        file: 'TestData.zip'
+        file: 'SampleData.zip'
 
     - name: Unzip assets
       shell: bash --login {0}
-      run: unzip TestData.zip
+      run: unzip SampleData.zip -d tests
 
     - name: Set up conda (Miniconda only)
       uses: conda-incubator/setup-miniconda@v2
@@ -47,14 +47,22 @@ jobs:
         ls -l $CONDA_PREFIX/include/htslib
         make CONDA_PREFIX=$CONDA_PREFIX
 
-    - name: Run unit tests
+    - name: Test installation
       shell: bash --login {0}
       run: |
         source $(conda info --base)/etc/profile.d/conda.sh
         conda activate contextsv
         ./build/contextsv --version
         ./build/contextsv --help
 
+    - name: Run tests
+      shell: bash --login {0}
+      run: |
+        source $(conda info --base)/etc/profile.d/conda.sh
+        conda activate contextsv
+        mkdir -p output
+        python -m pytest -s -v
+
       # run: |
       #   source $(conda info --base)/etc/profile.d/conda.sh
       #   conda activate contextsv

Dockerfile

@@ -0,0 +1,21 @@
+# Use the miniconda container
+FROM continuumio/miniconda3:main
+
+# Version argument (set during build)
+ARG CONTEXTSV_VERSION
+
+WORKDIR /app
+
+RUN apt-get update
+RUN conda update conda
+
+# Install ContextSV
+RUN conda config --add channels wglab
+RUN conda config --add channels conda-forge
+RUN conda config --add channels bioconda
+RUN conda create -n contextsv python=3.9
+RUN echo "conda activate contextsv" >> ~/.bashrc
+SHELL ["/bin/bash", "--login", "-c"]
+RUN conda install -n contextsv -c wglab -c conda-forge -c bioconda contextsv=${CONTEXTSV_VERSION} && conda clean -afy
+
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "contextsv", "contextsv"]

Makefile

@@ -4,13 +4,6 @@ SRC_DIR := $(CURDIR)/src
 BUILD_DIR := $(CURDIR)/build
 LIB_DIR := $(CURDIR)/lib
 
-# Version header
-VERSION := $(shell git describe --tags --always)
-VERSION_HEADER := $(INCL_DIR)/version.h
-.PHONY: $(VERSION_HEADER)
-	@echo "#pragma once" > $@
-	@echo "#define VERSION \"$(VERSION)\"" >> $@
-
 # Conda environment directories
 CONDA_PREFIX := $(shell echo $$CONDA_PREFIX)
 CONDA_INCL_DIR := $(CONDA_PREFIX)/include
@@ -50,4 +43,3 @@ $(BUILD_DIR)/%.o: $(SRC_DIR)/%.cpp
 # Clean the build directory
 clean:
 	rm -rf $(BUILD_DIR)
-	

README.md

@@ -13,8 +13,32 @@ Class documentation is available at <a href="https://wglab.openbioinformatics.or
 </p>
 
 ## Installation
+### Anaconda
+First, install [Anaconda](https://www.anaconda.com/).
 
-### Building from source (for testing/development)
+Next, create a new environment. This installation has been tested with Python 3.9, Linux 64-bit.
+
+```
+conda create -n contextsv python=3.9
+conda activate contextsv
+```
+
+ContextSV and its dependencies can then be installed using the following command:
+
+```
+conda install -c wglab -c conda-forge -c bioconda contextsv
+```
+
+### Docker
+First, install [Docker](https://docs.docker.com/engine/install/).
+Pull the latest image from Docker hub, which contains the latest release and its dependencies.
+
+```
+docker pull genomicslab/contextsv
+```
+
+
+## Building from source (for testing/development)
 ContextSV requires HTSLib as a dependency that can be installed using  [Anaconda](https://www.anaconda.com/). Create an environment
 containing HTSLib: 
 
@@ -42,7 +66,6 @@ Options:
   -s, --snp <vcf_file>          SNPs VCF file (required)
   -o, --outdir <output_dir>     Output directory (required)
   -c, --chr <chromosome>        Chromosome
-  -r, --region <region>         Region (start-end)
   -t, --threads <thread_count>  Number of threads
   -h, --hmm <hmm_file>          HMM file
   -n, --sample-size <size>      Sample size for HMM predictions