Merge pull request #424 from pangenome/update_stuff

latest vcflib
pangenome · Nov 1, 2024 · 4f1ba17 · 4f1ba17
2 parents 212dbb1 + 7f35ae6
commit 4f1ba17
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diff --git a/.github/workflows/build_and_test_docker.yml b/.github/workflows/build_and_test_docker.yml
@@ -11,11 +11,11 @@ jobs:
         run: docker build . --file Dockerfile --target binary --tag pggb
       - name: Run a test on the DRB1-3123 dataset (SPOA)
         run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -M -m -o drib1_spoa && ls drib1_spoa/* && head drib1_spoa/*.log -n 63"
-      - name: Run a test on the DRB1-3123 dataset (abPOA)
-        run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -M -m -b -o drib1_abpoa && ls drib1_abpoa/* && head drib1_abpoa/*.log -n 63"
+      - name: Run a test on the DRB1-3123 dataset (abPOA global)
+        run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -M -m  --global-poa -b -o drib1_abpoa && ls drib1_abpoa/* && head drib1_abpoa/*.log -n 63"
       - name: Run a test on the DRB1-3123 dataset (paf)
         run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -a data/paf/DRB1-3123.fa.15a1009.wfmash.paf -p 70 -s 3000 -G 2000 -n 10 -t 2 -Z -M -m -o drib1_paf && ls drib1_paf/* && head drib1_paf/*.log -n 63"
       - name: Run a test on the LPA dataset (SPOA global)
-        run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/LPA/LPA.fa.gz -p 95 -s 20000 -G 800,900 -k 79 -t 2 -Z -O 0.001 -m -z -o lpa -V 'chm13,chm1:1000' && ls lpa/* && head lpa/*.log -n 63"
+        run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/LPA/LPA.fa.gz -p 95 -s 20000 -G 800,900 -k 79 -t 2 -Z -O 0.001 -m --global-poa -o lpa -V 'chm13,chm1:1000' && ls lpa/* && head lpa/*.log -n 63"
       - name: Run a test for the gfa2evaluation script on a mini HPRC chrMT dataset
         run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "gfa2evaluation.sh data/chrM.pan.4.gfa chm13 data/test_eval 2"
diff --git a/Dockerfile b/Dockerfile
@@ -1,21 +1,23 @@
-FROM debian:bullseye-slim AS binary
+FROM debian:bookworm-slim AS binary
 
 LABEL authors="Erik Garrison, Simon Heumos, Andrea Guarracino"
 LABEL description="Preliminary docker image containing all requirements for pggb pipeline"
-LABEL base_image="debian:bullseye-slim"
+LABEL base_image="debian:bookworm-slim"
 LABEL software="pggb"
 LABEL about.home="https://github.com/pangenome/pggb"
 LABEL about.license="SPDX:MIT"
 
 # dependencies
 RUN apt-get update \
-    && apt-get install -y \
+    && apt-get install -y --no-install-recommends \
                        git \
                        bash \
                        cmake \
                        make \
                        g++-11 \
                        python3-dev \
+                       python3-pip \
+                       python3-venv \
                        pybind11-dev \
                        libbz2-dev \
                        bc \
@@ -38,6 +40,8 @@ RUN apt-get update \
                        libcairo2-dev \
                        unzip \
                        parallel \
+                       r-base \
+                       libclang-dev \
     && apt-get clean \
     && apt-get purge  \
     && rm -rf /var/lib/apt/lists/*
@@ -98,8 +102,6 @@ RUN git clone https://github.com/marschall-lab/GFAffix.git \
     && cd ../ \
     && rm -rf GFAffix
 
-RUN pip install multiqc==1.22.2
-
 RUN wget https://github.com/vgteam/vg/releases/download/v1.59.0/vg && chmod +x vg && mv vg /usr/local/bin/vg
 
 RUN git clone https://github.com/pangenome/vcfbub \
@@ -113,7 +115,7 @@ RUN git clone https://github.com/pangenome/vcfbub \
 
 RUN git clone --recursive https://github.com/vcflib/vcflib.git \
     && cd vcflib \
-    && git checkout 404b98a6a0601a8668fb039eae5196fa1ae12525 \
+    && git checkout 0272f2d8ebcb70ca9b7f23a0aed3991e0a63ae6b \
     && mkdir -p build \
     && cd build \
     && cmake -DZIG=OFF -DCMAKE_BUILD_TYPE=Debug -DWFA_GITMODULE=ON .. && cmake --build . -- -j $(nproc) \
@@ -122,10 +124,6 @@ RUN git clone --recursive https://github.com/vcflib/vcflib.git \
     && cd ../ \
     && rm -rf vcflib
 
-# Community detection dependencies
-RUN pip install igraph==0.11.5
-RUN pip install pycairo==1.26.1
-
 # Additional tools
 RUN git clone https://github.com/ekg/fastix.git \
     && cd fastix \
@@ -162,23 +160,24 @@ RUN wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.12.1/
     && unzip rtg-tools-3.12.1-linux-x64.zip && sed -i 's/read -r -p "Would you like to enable automatic usage logging (y\/n)? " REPLY/REPLY="n"/g' /rtg-tools-3.12.1/rtg \
     && ln -s /rtg-tools-3.12.1/rtg /usr/local/bin/ && rtg help
 
-# Install base R
-# NOTE: we might have to go the conda way on the long run
-# https://www.reddit.com/r/Rlanguage/comments/oi31xn/installing_r41_on_debian_bullseye_testing/
-RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-key B8F25A8A73EACF41 \
-    && echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" > /etc/apt/sources.list.d/r-packages.list \
-    && apt update \
-    && apt install -y r-base \
-    && apt-get clean \
-    && apt-get purge  \
-    && rm -rf /var/lib/apt/lists/* \
-    && wget https://cran.r-project.org/src/contrib/Archive/data.table/data.table_1.15.2.tar.gz \
-    && R CMD INSTALL data.table_1.15.2.tar.gz
+# Install R package
+RUN wget https://cran.r-project.org/src/contrib/Archive/data.table/data.table_1.15.2.tar.gz \
+    && R CMD INSTALL data.table_1.15.2.tar.gz \
+    && rm data.table_1.15.2.tar.gz
 
 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static \
     && mv bedtools.static /usr/local/bin/bedtools \
     && chmod +x /usr/local/bin/bedtools
 
+# Set up Python virtual environment
+RUN python3 -m venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Install Python packages in virtual environment
+RUN pip install multiqc==1.22.2 \
+    && pip install igraph==0.11.5 \
+    && pip install pycairo==1.26.1
+
 # copy required scripts
 COPY scripts/* /usr/local/bin/
 COPY scripts /usr/local/bin/scripts/