Update ksrates to version 2.0.0

.github/workflows/test_pipeline.yml

@@ -15,30 +15,41 @@ on:
 jobs:
   build:
     # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # Runs commands using the runners shell
       - name: Building dependency Docker container
         # Builds here the Docker container
         run: docker build . --file Dockerfile --tag ksrates
 
+      - name: Set Java 17 Environment
+        run: |
+          echo "JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64" >> $GITHUB_ENV
+          echo "/usr/lib/jvm/java-17-openjdk-amd64/bin" >> $GITHUB_PATH
+
       - name: Installing Nextflow
         run: |
           sudo apt-get update
-          sudo apt-get install wget default-jdk
+          sudo apt-get install wget openjdk-17-jdk
           sudo wget -qO- https://get.nextflow.io | bash
           sudo mv nextflow /usr/bin
 
       - name: Running ksrates Nextflow pipeline
         run: |
           cd test
-          mv nextflow.config custom_nextflow.config
-          NXF_VER=21.10.6 nextflow run ../main.nf --config config_elaeis.txt -with-docker ksrates
+          NXF_VER=24.10.5 nextflow run ../main.nf --test -profile docker --config config_files/config_elaeis.txt --expert config_files/config_expert.txt -with-docker ksrates
 
       - name: Visualize output files
         if: ${{ always() }}
         run: ls -l test/rate_adjustment/elaeis
+
+      - uses: actions/upload-artifact@v4
+        name: Test output files
+        if: ${{ always() }}
+        with:
+          name: ksrates_test_pipeline_output
+          path: test/rate_adjustment/elaeis/

.gitignore

@@ -1,9 +1,11 @@
 __pycache__
 .vscode
 .nextflow
+.nextflow.log*
 docs/outdir
-test/work
-test/.nextflow*
-test/ortholog_distributions
-test/.nextflow
 test/rate_adjustment
+test/ortholog_distributions
+test/work
+example/rate_adjustment
+example/ortholog_distributions
+example/work

.readthedocs.yaml

@@ -7,9 +7,9 @@ build:
 
 # Build from the docs/ directory with Sphinx
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/conf.py
 
 # Explicitly set the version of Python and its requirements
 python:
   install:
-    - requirements: doc/source/requirements.txt
+    - requirements: docs/requirements.txt

Dockerfile

@@ -1,27 +1,58 @@
-FROM vibpsb/i-adhore
+FROM vibpsb/i-adhore:3.1
 
 MAINTAINER Cecilia Sensalari
 
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
 ENV DEBIAN_FRONTEND=noninteractive
 
-# Install PAML from source
-
-RUN apt-get install -y wget && wget http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz && \
-	tar -xzf paml4.9j.tgz && cd paml4.9j/src && make -f Makefile && mv codeml /bin && cd /
-
-# Install Python3, wgd dependencies...
+# Install Python 3.9
+RUN apt-get update && \
+    apt-get install -y software-properties-common && \
+    add-apt-repository ppa:deadsnakes/ppa && \
+    apt-get update && \
+    apt-get install -y python3.9 python3.9-distutils && \
+	curl -sS https://bootstrap.pypa.io/get-pip.py | python3.9 && \
+	python3.9 -m pip install --upgrade pip
+
+# Install non-python wgd dependencies
+RUN apt-get update && apt-get install -yq \
+    wget \
+    git \
+    curl \
+    default-jdk \
+    build-essential \
+    mcl \
+    ncbi-blast+ \
+    muscle \
+    fasttree
 
-RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -yq install python3-pip python3-tk git curl \
-	default-jdk build-essential mcl ncbi-blast+ muscle mafft prank fasttree phyml
-
-ADD /requirements.txt /install/requirements.txt
-ADD /setup.py /install/setup.py
-ADD /ksrates /install/ksrates
-ADD /wgd_ksrates /install/wgd_ksrates
-ADD /README.md /install/README.md
-ADD /ksrates_cli.py /install/ksrates_cli.py
+# Install PAML from source
+RUN wget http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz && \
+    tar -xzf paml4.9j.tgz && cd paml4.9j/src && make -f Makefile && \
+    mv codeml /bin && cd /
+
+# Install DIAMOND
+RUN wget http://github.com/bbuchfink/diamond/releases/download/v2.1.9/diamond-linux64.tar.gz && \
+    tar -xzf diamond-linux64.tar.gz && mv diamond /bin
+
+# Install OrthoMCLight
+RUN wget https://raw.githubusercontent.com/VIB-PSB/OrthoMCLight/main/orthomclight.pl -P /bin && \
+    wget https://raw.githubusercontent.com/VIB-PSB/OrthoMCLight/main/orthomclight_module.pm -P /bin && \
+    chmod a+rx /usr/bin/orthomclight*
+
+# Download the 37 angiosperm sequence zipped file from Zenodo for the reciprocal retention pipeline
+RUN wget https://zenodo.org/records/15225340/files/original_angiosperm_sequences.tar.gz -P /ksrates/reciprocal_retention
+
+# Copy ksrates files
+ADD /requirements.txt /ksrates/requirements.txt
+ADD /setup.py /ksrates/setup.py
+ADD /ksrates /ksrates/ksrates
+ADD /wgd_ksrates /ksrates/wgd_ksrates
+ADD /README.md /ksrates/README.md
+ADD /ksrates_cli.py /ksrates/ksrates_cli.py
 
 # Install ksrates and requirements from requirements.txt
-RUN python3 -m pip install /install
+RUN python3.9 -m pip install -r /ksrates/requirements.txt && \
+    python3.9 -m pip install /ksrates && \
+    rm -r /ksrates