From 4a47f5c4c98343195740051297a2d10295385d6c Mon Sep 17 00:00:00 2001
From: "Godwin N. Ani" <aniigodwinn@gmail.com>
Date: Tue, 25 Mar 2025 17:49:21 -0400
Subject: [PATCH] Update Dockerfile.txt

---
 PTL2/Dockerfile.txt | 82 ++++++++++++++++-----------------------------
 1 file changed, 29 insertions(+), 53 deletions(-)

diff --git a/PTL2/Dockerfile.txt b/PTL2/Dockerfile.txt
index b62afd3..2f7f994 100644
--- a/PTL2/Dockerfile.txt
+++ b/PTL2/Dockerfile.txt
@@ -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"]