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Update Dockerfile.txt

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Godwin N. Ani 2025-03-25 17:49:21 -04:00 committed by GitHub
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PTL2/Dockerfile.txt
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@ -1,63 +1,23 @@
FROM python:3.8.20-bullseye
RUN apt-get update -y && apt-get upgrade -y && \
apt-get install git wget ncbi-blast+-legacy mafft build-essential vim -y
apt-get install -y \
git wget ncbi-blast+-legacy mafft build-essential vim unzip cmake gcc g++ \
libomp-dev libboost-all-dev libeigen3-dev cpanminus && \
rm -rf /var/lib/apt/lists/*
# EukPhylo installation
# Tested on: RUN git clone -b patch-1 https://github.com/DLBPointon/EukPhylo.git
# Install python dependencies
# Install Python dependencies
RUN pip install biopython==1.75 ete3==3.1.2 tqdm==4.66.4 six==1.17.0
RUN git clone -b Docker https://github.com/Katzlab/EukPhylo.git
# Install dependencies
RUN apt-get update && apt-get install -y \
unzip \
cmake \
gcc \
g++ \
libomp-dev \
libboost-all-dev \
libeigen3-dev \
&& rm -rf /var/lib/apt/lists/*
# Clone IQ-TREE 2 repository with submodules and compile it
RUN git clone --recursive https://github.com/iqtree/iqtree2.git && \
cd iqtree2 && \
git checkout v2.4.0 && \
mkdir build && cd build && \
cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ .. && \
make -j$(nproc) && \
make install && \
cd ../.. && rm -rf iqtree2
# VSEARCH installation
RUN wget https://github.com/torognes/vsearch/releases/download/v2.21.0/vsearch-2.21.0-linux-aarch64.tar.gz && \
tar xzf vsearch-2.21.0-linux-aarch64.tar.gz && \
mv vsearch-2.21.0-linux-aarch64 /usr/local/vsearch && \
ln -s /usr/local/vsearch/bin/vsearch /usr/local/bin/vsearch
# Guidance installation
RUN mkdir guidance && \
wget https://taux.evolseq.net/guidance/static/download/guidance.v2.02.tar.gz && \
tar -xzvf guidance.v2.02.tar.gz -C guidance --no-same-owner && \
cd guidance/guidance.v2.02 && make
# Guidance installation and debug for 'guidance.pl' file existence
RUN git clone https://github.com/anzaika/guidance.git && \
cd guidance && make
# Guidance bio perl dependency
RUN apt-get update && apt-get install -y cpanminus && \
cpanm Bio::Perl
# Clean the container
RUN rm -rf vsearch-2.21.0-linux-aarch64.tar.gz guidance.v2.02.tar.gz
# Download and compile TrimAl from source
# TrimAl installation
RUN wget -O trimal-1.5.0.zip https://github.com/inab/trimal/archive/refs/tags/v1.5.0.zip && \
unzip trimal-1.5.0.zip && \
cd trimal-1.5.0/source && \
@ -72,15 +32,31 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree && \
chmod +x FastTree && \
mv FastTree /usr/local/bin/
# Clone IQ-TREE 2 repository and compile it
RUN git clone --recursive https://github.com/iqtree/iqtree2.git && \
cd iqtree2 && \
git checkout v2.4.0 && \
mkdir build && cd build && \
cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ .. && \
make -j$(nproc) && \
make install && \
cd ../.. && rm -rf iqtree2
# Add executables to path
# Clean the container
RUN rm -rf vsearch-2.21.0-linux-aarch64.tar.gz
# EukPhylo installation
RUN git clone -b Docker https://github.com/Katzlab/EukPhylo.git
# Add executables to PATH
ENV PATH="$PATH:/iqtree/bin/iqtree:/usr/local/vsearch/bin/vsearch:/usr/local/trimal/trimal:/usr/local/bin"
# Change executable permissions on wrapper script
RUN ["chmod", "+x", "/EukPhylo/PTL2/run_eukphylo.sh"]
# Change executable permissions on guidance
RUN ["chmod", "+x", "/guidance/guidance.v2.02/www/Guidance/guidance.pl"]
# Change executable permissions on guidance.pl after confirming its existence
RUN ["chmod", "+x", "/guidance/www/Guidance/guidance.pl"]
# Change entrypoint on execution of the container
ENTRYPOINT ["bash","/EukPhylo/PTL2/run_eukphylo.sh"]
ENTRYPOINT ["bash", "/EukPhylo/PTL2/run_eukphylo.sh"]