From 742eb7008a21910c95a5861c0dbb91d08f995d76 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Tue, 25 Feb 2025 10:42:23 +0000
Subject: [PATCH] Create Dockerfile

---
 PTL2/Dockerfile | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 PTL2/Dockerfile

diff --git a/PTL2/Dockerfile b/PTL2/Dockerfile
new file mode 100644
index 0000000..0deba38
--- /dev/null
+++ b/PTL2/Dockerfile
@@ -0,0 +1,47 @@
+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
+
+# PhyloToL installation
+# Tested on: RUN git clone -b patch-1 https://github.com/DLBPointon/EukPhylo.git
+# Will work on below container after PR merge
+
+RUN git clone -b Docker https://github.com/Katzlab/EukPhylo.git
+
+# IQ-TREE installation
+RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz && \
+    tar xzf iqtree-1.6.12-Linux.tar.gz && \
+    mv iqtree-1.6.12-Linux/ /usr/local/iqtree && \
+    ln -s /usr/local/iqtree/bin/iqtree /usr/local/bin/iqtree
+
+# Install python dependencies
+RUN pip install biopython==1.75 ete3==3.1.2 tqdm==4.66.4 six==1.17.0
+
+# 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
+
+# Install pre-compiled version of Trimal 1.5.0
+RUN wget https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip && \
+    unzip trimAl_Linux_x86-64.zip && \
+    mv trimAl_Linux_x86-64 /usr/local/trimal
+
+# Clean the container
+RUN rm -rf iqtree-1.6.12-Linux.tar.gz vsearch-2.21.0-linux-aarch64.tar.gz guidance.v2.02.tar.gz trimAl_Linux_x86-64.zip
+
+# 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 entrypoint on execution of the container
+ENTRYPOINT ["bash","/EukPhylo/PTL2/run_eukphylo.sh"]