Manuscript update #17

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Merged

jonperdomo merged 21 commits into main from manuscript-update

Sep 20, 2025

.github/workflows/build-tests.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -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

-Original file line number
+Diff line change
@@ -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

-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand Down Expand Up / @@ -50,4 +43,3 @@ $(BUILD_DIR)/%.o: $(SRC_DIR)/%.cpp @@
     # Clean the build directory
     clean:
     	rm -rf $(BUILD_DIR)

README.md

-Original file line number
+Diff line change
@@ Expand Up @@
     </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:
@@ Expand Down Expand Up / @@ -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
@@ Expand Down @@

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