phylogenomics.def

Bootstrap: docker
From: ubuntu:22.04

%post
apt-get update
apt-get install -y build-essential
apt-get install -y git
apt-get install -y python3
apt-get install -y libterm-readline-gnu-perl
apt-get -y install python3-pip
apt-get install wget
apt-get install g++
apt-get install unzip
pip3 install clipkit
cd /opt
git clone https://github.com/chaoszhang/ASTER.git
cd ASTER
make

mkdir /opt/orthofinder && cd /opt/orthofinder
wget https://github.com/davidemms/OrthoFinder/releases/download/2.5.5/OrthoFinder.tar.gz
tar zxvf OrthoFinder.tar.gz
cd OrthoFinder

mkdir /opt/raxml && cd /opt/raxml
wget https://github.com/amkozlov/raxml-ng/releases/download/1.2.2/raxml-ng_v1.2.2_linux_x86_64.zip
unzip raxml-ng_v1.2.2_linux_x86_64.zip


mkdir /opt/alignment && cd /opt/alignment
git clone https://github.com/inab/trimal.git
cd trimal/source
make
cd /opt/alignment

git clone https://github.com/codecreatede/alignmentGo.git

%environment
export PATH=/opt/ASTER/bin:$PATH
export PATH=/opt/orthofinder/OrthoFinder:$PATH
export PATH=/opt/raxml:$PATH
export PATH=/opt/alignment/trimal/source:$PATH
export PATH=/opt/alignment/alignmentGo:$PATH

%labels
Author Gaurav Sablok
Contact: gauravcodepro@gmail.com
This is the apptainer compilation for phylogenomics. This single container has
all the phylogenomics tools compiled and enabled for the phylogenomics. It includes
the orthology analysis ASTRAL species tree estimation, boostrapping phylogenies using
the RAXML and the alignment analysis using the trimal and the alignmentGO.

%help
Given an folder of the fasta file you can invoke the apptainer orthofinder as
apptainer run phylogenomics.sif orthofinder PATH-FASTA-FOLDER
apptainer run phylogenomics.sif astral -h
apptainer run phylogenomics.sif trimal -h
apptainer run phylogenomics.sif alignmentGO -h