实验记录 | Shimmer的安装

参考链接：
https://mybiosoftware.com/shimmer-detection-of-genetic-alterations-in-tumors-using-next-generation-sequence-data.html

https://research.nhgri.nih.gov/software/Shimmer/download.shtml

https://github.com/nhansen/Shimmer

1。搭建依赖环境

安装R语言以及statmod包。
因为之前已经安装了conda，所以只需要用conda安装即可，非常方便。但是，安装得到的R并不能更新到最新版。好在这个软件对于R的版本要求并不是很高。
conda R
R安装成功！

R version 3.6.1 (2019-07-05) – “Action of the Toes”
Copyright © 2019 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type ‘license()’ or ‘licence()’ for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type ‘contributors()’ for more information and
‘citation()’ on how to cite R or R packages in publications.
Type ‘demo()’ for some demos, ‘help()’ for on-line help, or
‘help.start()’ for an HTML browser interface to help.
Type ‘q()’ to quit R.

在这个基础上，安装statmod包。
即，在R的环境中，输入install.packages(statmod)即可。

2。安装shimmer

perl Build.PL --install_base $HOME

Can’t locate Module/Build.pm in @INC (you may need to install the Module::Build module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at Build.PL line 3.
BEGIN failed–compilation aborted at Build.PL line 3.

线索：you may need to install the Module::Build module
bing搜索引擎的检索效果要比百度搜索的精准度更高。

如何安装Build 这样一个模块？
找到这样一个页面：https://metacpan.org/pod/Module::Build
并且按照链接https://www.cpan.org/modules/INSTALL.html指示安装模块。
cpan App:cpanminus
sudo cpanm Module::Build
模块下载完成。

–> Working on Module::Build
Fetching http://www.cpan.org/authors/id/L/LE/LEONT/Module-Build-0.4231.tar.gz … OK
Configuring Module-Build-0.4231 … OK
Building and testing Module-Build-0.4231 … OK
Successfully installed Module-Build-0.4231
1 distribution installed

重新运行perl代码。
perl Build.PL --install_base $HOME
./Build
./Build test
./Build install
export PATH=$HOME/bin:$PATH
export PERL5LIB=$HOME/lib/perl5:$PERL5LIB

到这里，基本安装完成。
perl shimmer.pl

Usage: shimmer.pl <–region chr1:1000-2000> <–bedfile bed file of regions> <–ref reference fasta>
For more information, type “perldoc shimmer.pl”. at shimmer.pl line 49.