genomeannotate.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
mkdir /opt/compleasm
cd /opt/compleasm
wget https://github.com/huangnengCSU/compleasm/releases/download/v0.2.6/compleasm-0.2.6_x64-linux.tar.bz2
tar -jxvf compleasm-0.2.6_x64-linux.tar.bz2
cd /opt
mkdir /opt/seppinstall
cd /opt/seppinstall
git clone https://github.com/smirarab/sepp.git
cd sepp
python3 setup.py config -c
python3 setup.py install
cd /opt/
mkdir /opt/hmmer
cd /opt/hmmer
wget http://eddylab.org/software/hmmer/hmmer.tar.gz
tar zxf hmmer.tar.gz
cd hmmer-3.4
./configure --prefix /opt/hmmer
make
make check
make install
cd /opt/
mkdir /opt/miniprotinstall
cd /opt/miniprotinstall
git clone https://github.com/lh3/miniprot
cd miniprot && make
%environment
export PATH=/opt/compleasm/compleasm_kit:$PATH
export PATH=/opt/seppinstall/sepp/:$PATH
export PATH=/opt/hmmer/:$PATH
export PATH=/opt/miniprotinstall/miniprot:$PATH
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Author Gaurav Sablok
Contact: gauravcodepro@gmail.com
This is the apptainer compilation for genome completeness, phylogenomics profiling.
It includes the genome annotation and phylogenomic profiling.