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INSTALL
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INSTALL
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#!/bin/bash
chmod 700 -R $HOME/sara/scripts
MYSHELL=$(echo $SHELL | awk -F/ '{print $NF}')
sudo apt-get install libz-dev
if [[ -z $(which sara) ]]; then
echo 'export PATH=$HOME/sara/scripts:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/."$MYSHELL"rc
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' >> $HOME/."$MYSHELL"rc
export PATH=$HOME/miniconda3/bin:/usr/local/share/rsi/idl/bin:$PATH
conda install -y -c conda-forge mamba
mamba update -y -n base -c conda-forge -c anaconda -c bioconda -c defaults conda
mamba create -y -n sara_dge -c r -c conda-forge -c anaconda -c bioconda -c defaults bioconductor-deseq2 bioconductor-edger bioconductor-enhancedvolcano bioconductor-genefilter bioconductor-vsn boost-cpp r-ashr r-base=4.1 r-biocmanager r-calibrate r-devtools r-ggplot2 r-gplots r-pheatmap r-rcolorbrewer r-remotes
mamba create -y -n sara_prep -c conda-forge -c anaconda -c bioconda -c defaults bowtie2 fastp fastqc hisat2 multiqc rsem trimmomatic star
elif [[ -z $(which mamba) ]]; then
conda install -y -c conda-forge mamba
mamba update -y -n base -c conda-forge -c anaconda -c bioconda -c defaults conda
if [[ -z $(conda env list | grep sara_dge) ]]; then
mamba create -y -n sara_dge -c r -c conda-forge -c anaconda -c bioconda -c defaults bioconductor-deseq2 bioconductor-edger bioconductor-enhancedvolcano bioconductor-genefilter bioconductor-vsn boost-cpp r-ashr r-base=4.1 r-biocmanager r-calibrate r-devtools r-ggplot2 r-gplots r-pheatmap r-rcolorbrewer r-remotes
fi
if [[ -z $(conda env list | grep sara_prep) ]]; then
mamba create -y -n sara_prep -c conda-forge -c anaconda -c bioconda -c defaults bowtie2 fastp fastqc hisat2 multiqc rsem trimmomatic star
fi
elif [[ ! -z $(which mamba) ]]; then
if [[ -z $(conda env list | grep sara_dge) ]]; then
mamba create -y -n sara_dge -c r -c conda-forge -c anaconda -c bioconda -c defaults bioconductor-deseq2 bioconductor-edger bioconductor-enhancedvolcano bioconductor-genefilter bioconductor-vsn boost-cpp r-ashr r-base=4.1 r-biocmanager r-calibrate r-devtools r-ggplot2 r-gplots r-pheatmap r-rcolorbrewer r-remotes
fi
if [[ -z $(conda env list | grep sara_prep) ]]; then
mamba create -y -n sara_prep -c conda-forge -c anaconda -c bioconda -c defaults bowtie2 fastp fastqc hisat2 multiqc rsem trimmomatic star
fi
conda --version && mamba --version | sed '2d' && echo "" && echo "conda environments:" && conda env list | egrep 'sara'
fi
if [[ -z $(which featureCounts) ]]; then
FC_VERSION=2.0.3
cd
wget https://ufpr.dl.sourceforge.net/project/subread/subread-"$FC_VERSION"/subread-"$FC_VERSION"-source.tar.gz --no-check-certificate
tar -xvf subread-"$FC_VERSION"-source.tar.gz
rm subread-"$FC_VERSION"-source.tar.gz
mv subread-"$FC_VERSION"-source subread-source
cd subread-source/src
make -f Makefile.Linux
echo 'export PATH=$HOME/subread-source/bin:/usr/local/share/rsi/idl/bin:$PATH' >> $HOME/."$MYSHELL"rc
export PATH=$HOME/subread-source/bin:/usr/local/share/rsi/idl/bin:$PATH
else
featureCounts -v
fi