genome MuSic安装

Posted 2020-07-21 qinqinyang

系统：ubuntu 15.04
全程在root权限下安装 

首先安装软件samtools ，必须是samtools-0.1.19 版本
tar jxf samtools-0.1.19.tar.bz2
cd samtools-0.1.19
make
export SAMDIR=$PWD
sudo mv samtools /usr/local/bin/
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#安装相关依赖包

sudo apt-get install curl gcc make perl git  libbam-dev bedtools r-base-core libexpat1-dev zlib1g-dev tabix
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#安装 joinx

git clone --recursive https://github.com/genome/joinx.git
sudo apt-get install build-essential cmake libbz2-dev libgtest-dev
cd joinx
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=release
make deps
make
sudo make install

# 如果出现CMake Error at CMakeLists.txt:17 TestHelper等
#执行下列命令:
#git submodule update --init

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#安装calc-roi-covg
git clone https://github.com/ding-lab/calc-roi-covg.git

cd calc-roi-covg; make

sudo mv calcRoiCovg /usr/local/bin/

Install some R packages that enable parallelization across cores:

curl -LO "http://cran.r-project.org/src/contrib/{multicore_0.2.tar.gz,iterators_1.0.7.tar.gz,foreach_1.4.2.tar.gz,doMC_1.3.3.tar.gz}"
#multicore_0.2.tar.gz 该网页压缩包不存在 ，需要从其他网页下载
#iterators_1.0.8.tar.gz,foreach_1.4.3.tar.gz,doMC_1.3.4.tar.gz

sudo R CMD INSTALL multicore_0.2.tar.gz iterators_1.0.8.tar.gz foreach_1.4.3.tar.gz doMC_1.3.4.tar.gz

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#安装perl依赖包

curl -L http://cpanmin.us | sudo perl - --self-upgrade

Install some prerequisite Perl modules:

sudo `which cpanm` -n Text::CSV_XS Statistics::Distributions Statistics::Descriptive PDL PDL::Stats Module::Build Regexp::Common Time::HiRes IPC::Cmd LWP::Simple List::MoreUtils Set::Scalar Bit::Vector UR

sudo `which cpanm` -n http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome/genome_0.80.1-3.tar.gz

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#Install MuSiC:

sudo `which cpanm` -n http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome-music/genome-music_0.4.1-1.tar.gz

#安装完成，测试命令

genome music --help