From 87da279093822100ebb8f5f13519da7ea90fe9e3 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Fri, 14 Mar 2025 14:52:28 -0400 Subject: [PATCH] Delete PTL2/Dockerfile --- PTL2/Dockerfile | 47 ----------------------------------------------- 1 file changed, 47 deletions(-) delete mode 100644 PTL2/Dockerfile diff --git a/PTL2/Dockerfile b/PTL2/Dockerfile deleted file mode 100644 index 0deba38..0000000 --- a/PTL2/Dockerfile +++ /dev/null @@ -1,47 +0,0 @@ -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"]