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INSTALL
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INSTALL
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#!/bin/bash
sudo apt-get install -y \
autoconf \
automake \
build-essential \
ca-certificates \
cargo \
clang \
cmake \
curl \
dos2unix \
git \
libclang-dev \
libhdf5-dev \
libssl-dev \
libzstd-dev \
zlib1g-dev \
xz-utils
chmod 700 -R $HOME/vigeas/scripts
if [[ -z $(grep vigeas ~/.[bz]shrc) ]]; then
echo 'export PATH=$HOME/vigeas/scripts:$PATH' >> ~/.[bz]shrc
fi
if [[ -z $(which $HOME/.local/bin/micromamba) ]]; then
yes | "${SHELL}" <(curl -L micro.mamba.pm/install.sh)
echo 'alias conda=micromamba' >> ~/.[bz]shrc
echo 'alias mamba=micromamba' >> ~/.[bz]shrc
echo 'export PATH=$HOME/.local/bin:$PATH' >> ~/.[bz]shrc
export PATH=$HOME/.local/bin:$PATH
micromamba create -y -n vigeas-dnap -c conda-forge -c bioconda blast bwa fastp ivar mafft samtools seqkit
micromamba create -y -n vigeas-ont -c defaults -c conda-forge -c bioconda artic-porechop=0.3.2pre artic-tools=0.2.6 bcftools=1.17 biopython=1.81 bwa=0.7.17 clint=0.5.1 htslib=1.17 keras-preprocessing=1.1.2 longshot=0.4.5 mafft medaka minimap2=2.26 multiqc=1.15 muscle=3.8 nanopolish=0.14.0 ncurses=6.4=hcb278e6_0 pandas=2.0.3 pip pyfaidx=0.6.0 pytest python=3.9.15 pysam=0.21.0 pyvcf=0.6.8 requests=2.31.0 samtools=1.17 seqkit tqdm=4.66.1
micromamba create -y -n vigeas-rnapenr -c conda-forge -c bioconda blast bwa entrez-direct exonerate fastp ivar mafft samtools seqkit seqtk spades
micromamba create -y -n vigeas-sars2 -c conda-forge -c bioconda nextclade pangolin
micromamba create -y -n vigeas-stats -c conda-forge -c bioconda exonerate ghostscript r-base r-cowplot r-dplyr r-ggplot2 r-patchwork r-plyr r-readr r-svglite samtools seqkit seqtk
cd; git clone https://github.com/artic-network/fieldbioinformatics; cd fieldbioinformatics
python3 setup.py install
else
if [[ -z $(micromamba env list | grep vigeas-dnap) ]]; then
micromamba create -y -n vigeas-dnap -c conda-forge -c bioconda blast bwa fastp ivar mafft samtools seqkit
fi
if [[ -z $(micromamba env list | grep vigeas-ont) ]]; then
micromamba create -y -n vigeas-ont -c defaults -c conda-forge -c bioconda artic-porechop=0.3.2pre artic-tools=0.2.6 bcftools=1.17 biopython=1.81 bwa=0.7.17 clint=0.5.1 htslib=1.17 keras-preprocessing=1.1.2 longshot=0.4.5 mafft medaka minimap2=2.26 multiqc=1.15 muscle=3.8 nanopolish=0.14.0 ncurses=6.4=hcb278e6_0 pandas=2.0.3 pip pyfaidx=0.6.0 pytest python=3.9.15 pysam=0.21.0 pyvcf=0.6.8 requests=2.31.0 samtools=1.17 seqkit tqdm=4.66.1
cd; git clone https://github.com/artic-network/fieldbioinformatics; cd fieldbioinformatics
python3 setup.py install
fi
if [[ -z $(micromamba env list | grep vigeas-rnapenr) ]]; then
micromamba create -y -n vigeas-rnapenr -c conda-forge -c bioconda blast bwa entrez-direct exonerate fastp ivar mafft samtools seqkit seqtk spades
fi
if [[ -z $(micromamba env list | grep vigeas-sars2) ]]; then
micromamba create -y -n vigeas-sars2 -c conda-forge -c bioconda nextclade pangolin
fi
if [[ -z $(micromamba env list | grep vigeas-stats) ]]; then
micromamba create -y -n vigeas-stats -c conda-forge -c bioconda exonerate ghostscript r-base r-cowplot r-dplyr r-ggplot2 r-patchwork r-plyr r-readr r-svglite samtools seqkit seqtk
fi
echo "micromamba:" && micromamba --version && echo "" && echo "environments:" && micromamba env list | grep vigeas
fi
GUPPY_VERSION=6.5.7 # Archived Software
if [[ ! -z $(which guppy_basecaller) ]]; then
cd
wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_"$GUPPY_VERSION"_linux64.tar.gz -O ont-guppy.tar.gz
tar -vzxf ont-guppy.tar.gz
rm -rf ont-guppy.tar.gz
echo 'export PATH=$HOME/ont-guppy/bin:$PATH' >> ~/.[bz]shrc
elif [[ $(guppy_barcoder --version | awk -F" " '{print $NF}' | awk -F+ '{print $1}' | sed -n '1p') != "$GUPPY_VERSION" ]]; then
cd
rm -rf ont-guppy
wget https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy_"$GUPPY_VERSION"_linux64.tar.gz -O ont-guppy.tar.gz
tar -vzxf ont-guppy.tar.gz
rm -rf ont-guppy.tar.gz
else
guppy_basecaller --version
fi
DORADO_VERSION=0.6.0 # Updated 20 Apr 2024
if [[ ! -z $(which dorado) ]]; then
cd
wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-"$DORADO_VERSION"-linux-x64.tar.gz -O dorado.tar.gz
tar -vzxf dorado.tar.gz
rm -rf dorado.tar.gz
mv dorado-"$DORADO_VERSION"-linux-x64 ont-dorado
echo 'export PATH=$HOME/ont-dorado/bin:$PATH' >> ~/.[bz]shrc
export PATH=$HOME/ont-dorado/bin:$PATH
dorado download --directory ont-dorado/models
pip install pod5
echo 'export PATH=$HOME/.local/bin:$PATH' >> ~/.[bz]shrc
elif [[ $(dorado --version 2>&1 | awk -F+ '{print $1}') != "$DORADO_VERSION" ]]; then
cd
rm -rf ont-dorado
wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-"$DORADO_VERSION"-linux-x64.tar.gz -O dorado.tar.gz
tar -vzxf dorado.tar.gz
rm -rf dorado.tar.gz
mv dorado-"$DORADO_VERSION"-linux-x64 ont-dorado
export PATH=$HOME/ont-dorado/bin:$PATH
dorado download --directory ont-dorado/models
pip install pod5
else
dorado --version
fi