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INSTALL
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INSTALL
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#!/bin/bash
sudo apt-get install build-essential cargo clang curl git libclang-dev zlib1g-dev xz-utils
chmod 700 -R $HOME/vgapONT/scripts
if [[ -z $(which vgapONT) ]]; then
echo 'export PATH=$HOME/vgapONT/scripts:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/.$(basename $SHELL)rc
fi
GUPPY_VERSION=6.2.1 # Updated Ago 15 2022
if [[ -z $(which guppy_basecaller) ]]; then
cd
wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_"$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=$HOME/ont-guppy/bin:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/.$(basename $SHELL)rc
source $HOME/.$(basename $SHELL)rc
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://mirror.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:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/.$(basename $SHELL)rc
source $HOME/.$(basename $SHELL)rc
else
guppy_basecaller --version
fi
if [[ -z $(which conda) ]]; then
cd
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -bfp miniconda3
rm Miniconda3-latest-Linux-x86_64.sh
echo 'export PATH=$HOME/miniconda3/bin:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/.$(basename $SHELL)rc
source $HOME/.$(basename $SHELL)rc
conda install -y -c conda-forge mamba
mamba update -y -c conda-forge -c anaconda -c bioconda -c defaults -n base conda
mamba create -y -n vgap_assembly -c conda-forge -c anaconda -c bioconda -c defaults artic exonerate medaka mafft seqkit seqtk
mamba create -y -n vgap_qc -c conda-forge -c anaconda -c bioconda -c defaults python=3.6 pycoqc
mamba create -y -n vgap_plot -c conda-forge -c anaconda -c bioconda -c defaults ghostscript numpy pandas pysam seaborn
elif [[ -z $(which mamba) ]]; then
conda install -y -c conda-forge mamba
mamba update -y -c conda-forge -c anaconda -c bioconda -c defaults -n base conda
if [[ -z $(conda env list | grep vgap_assembly) ]]; then
mamba create -y -n vgap_assembly -c conda-forge -c anaconda -c bioconda -c defaults artic exonerate medaka mafft seqkit seqtk
fi
if [[ -z $(conda env list | grep vgap_qc) ]]; then
mamba create -y -n vgap_qc -c conda-forge -c anaconda -c bioconda -c defaults python=3.6 pycoqc
fi
if [[ -z $(conda env list | grep vgap_plot) ]]; then
mamba create -y -n vgap_plot -c conda-forge -c anaconda -c bioconda -c defaults ghostscript numpy pandas pysam seaborn
fi
elif [[ ! -z $(which mamba) ]]; then
if [[ -z $(conda env list | grep vgap_assembly) ]]; then
mamba create -y -n vgap_assembly -c conda-forge -c anaconda -c bioconda -c defaults artic exonerate medaka mafft seqkit seqtk
fi
if [[ -z $(conda env list | grep vgap_qc) ]]; then
mamba create -y -n vgap_qc -c conda-forge -c anaconda -c bioconda -c defaults python=3.6 pycoqc
fi
if [[ -z $(conda env list | grep vgap_plot) ]]; then
mamba create -y -n vgap_plot -c conda-forge -c anaconda -c bioconda -c defaults ghostscript numpy pandas pysam seaborn
fi
conda --version && mamba --version | sed '2d' && echo "" && echo "conda environments:" && conda env list | grep vgap
fi
if [[ -z $(which fastcov.py) ]]; then
cd
git clone https://github.com/RaverJay/fastcov
cd fastcov
echo 'export PATH=$HOME/fastcov:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/.$(basename $SHELL)rc
source $HOME/.$(basename $SHELL)rc
else
echo "" && echo "RaverJay/fastcov v0.1.3"
fi
if [[ -z $(which longshot) ]]; then
cd
wget https://github.com/pjedge/longshot/archive/refs/tags/v0.4.3.tar.gz
tar -xvf v0.4.3.tar.gz
cd cd longshot-0.4.3
cargo install --path .
echo 'export PATH=$HOME/.cargo/bin:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/.$(basename $SHELL)rc
source $HOME/.$(basename $SHELL)rc
else
longshot --version
fi