Install

#!/bin/bash

shopt -s expand_aliases

alias ~=”:«’~bash’”

:«’~~~bash’

Usage

sudo ./install.md core sx

Introduction

Install the project. Two modules can be installed. The core module install necessary environments, the chimeric aligner engine rearr, the demultiplex scripts, and other general auxiliary scripts. The sx module are in-house scripts specific to the data of sx and lcy.

Source

# Exit when fail.
set -e

for target in $@
do
    case $target in
        apt|core)
            apt-get update && apt-get install -y --no-install-recommends unzip build-essential libncurses5-dev gawk cutadapt samtools cmake bedtools
            ;;&
        bowtie2|core)
            cd dependencies/bowtie2-2.5.4-linux-x86_64
            for file in $(ls); do cp $file /usr/local/bin/; done
            cd -
            ;;&
        rearrangement|Rearrangement|core)
            mkdir -p core/Rearrangement/build
            cd core/Rearrangement/build
            cmake -DCMAKE_BUILD_TYPE=Release ..
            make
            make install
            cd -
            cp core/Rearrangement/correct_micro_homology.awk /usr/share/awk/
            ;;&
        removeDup|core)
            cp core/removeDuplicates.md /usr/local/bin/
            ;;&
        demultiplex|core)
            cp core/demultiplex/demultiplex.md /usr/local/bin/
            cp core/demultiplex/getAlignPos.awk /usr/share/awk/
            ;;&
        sx)
            # install getSxCsvFileRef
            cp sx/getSxCsvFileRef/getSxCsvFileRef.md /usr/local/bin/
            cp sx/getSxCsvFileRef/getSxCsvFileTarget.pl /usr/local/bin/
            cp sx/getSxCsvFileRef/getSxRefFile.pl /usr/local/bin/
            cp sx/getSxCsvFileRef/sxTargetSam2Bed.awk /usr/share/awk/
            # install cutR2Adapter
            cp sx/sxCutR2AdapterFilterCumulate/sxCutR2AdapterFilterCumulate.md /usr/local/bin/
            cp sx/sxCutR2AdapterFilterCumulate/sxCumulateToMapCutAdaptSpliter.awk /usr/share/awk/
            # install sxInderSpliter
            cp sx/sxExtractSpliter.md /usr/local/bin/
            ;;&
    esac
done

alias ~~~=":" # This suppresses a warning and is not part of source.