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dependencies.sh
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dependencies.sh
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#!/bin/bash -
#===============================================================================
#
# FILE: dependencies.sh
#
# USAGE: ./dependencies.sh
#
# DESCRIPTION: install a bunch of dependencies not installable through conda
#
# OPTIONS: ---
# AUTHOR: Q. ROUGEMONT
# ORGANIZATION: CNRS
# CREATED: 29/08/2024 10:18:12
#===============================================================================
# - Jellyfish install :
command='jellyfish'
if ! command -v $command &> /dev/null
then
echo "$command could not be found"
echo "will try a manual installation"
mkdir softs
cd softs
wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/jellyfish-2.3.1.tar.gz
tar zxvf jellyfish-2.3.1.tar.gz
cd jellyfish-2.3.1
./configure --prefix=$(pwd)
make -j8
if ! make install ; then
echo "installation of $command failed"
exit 1
fi
cd bin/
path=$(pwd)
echo -e "\n#Path to $command\nexport PATH=\$PATH:$path" >> ~/.bashrc
source ~/.bashrc
cd ../../../
fi
#activate env to have pandas
eval "$(conda shell.bash hook)"
conda activate assembly_env_full
# - compleasm (faster than the slow BUSCO) :
command='compleasm.py'
if ! command -v $command &> /dev/null
then
echo "$command could not be found"
echo "will try a manual installation"
mkdir softs 2>/dev/null
cd softs
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 compleasm_kit
if ! ./compleasm.py 1>/dev/null ; then
echo "installation of $command failed"
exit 1
fi
path=$(pwd)
echo -e "\n#Path to $command\nexport PATH=\$PATH:$path" >> ~/.bashrc
echo "sourcing bashrc"
source ~/.bashrc
cd ../../
fi
# - dorado for ONT base calling :
command='dorado'
if ! command -v $command &> /dev/null
then
echo "$command could not be found"
echo "will try a manual installation"
mkdir softs 2>/dev/null
cd softs 2>/dev/null
# - Dorado install :
wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-0.7.3-linux-x64.tar.gz
tar zxvf dorado-0.7.3-linux-x64.tar.gz
cd dorado-0.7.3-linux-x64/bin
if ! ./dorado 2>/dev/null ; then
echo "installation of $command failed"
exit 1
fi
path=$(pwd)
echo -e "\n#Path to $command\nexport PATH=\$PATH:$path" >> ~/.bashrc
source ~/.bashrc
cd ../../../
fi
# - CRAQ install :
#install pycircos first (not installed in the env):
pip install python-circos
command='craq'
if ! command -v $command &> /dev/null
then
echo "$command could not be found"
echo "will try a manual installation"
mkdir softs 2>/dev/null
cd softs 2>/dev/null
git clone https://github.com/JiaoLaboratory/CRAQ.git
cd CRAQ/Example/ && rm -rf Output
if ! bash run_example.sh ; then
echo "installation of $command failed"
exit 1
fi
cd ../bin
chmod +x craq
path=$(pwd)
echo -e "\n#Path to $command\nexport PATH=\$PATH:$path" >> ~/.bashrc
source ~/.bashrc
cd ../../
fi