GISTIC2.0初使用

我的操作系统：Ubuntu 16.04 LTS

GISTIC2.0用以分析癌症拷贝数变异的一个数据处理模块。具体介绍如下——
Summary:
The GISTIC module identifies regions of the genome that are significantly amplified or deleted across a set of samples. Each aberration is assigned a G-score that considers the amplitude of the aberration as well as the frequency of its occurrence across samples. False Discovery Rate q-values are then calculated for the aberrant regions, and regions with q-values below a user-defined threshold are considered significant. For each significant region, a “peak region” is identified, which is the part of the aberrant region with greatest amplitude and frequency of alteration. In addition, a “wide peak” is determined using a leave-one-out algorithm to allow for errors in the boundaries in a single sample. The “wide peak” boundaries are more robust for identifying the most likely gene targets in the region. Each significantly aberrant region is also tested to determine whether it results primarily from broad events (longer than half a chromosome arm), focal events, or significant levels of both. The GISTIC module reports the genomic locations and calculated q-values for the aberrant regions. It identifies the samples that exhibit each significant amplification or deletion, and it lists genes found in each “wide peak” region.
References:
Mermel C, Schumacher S, et al. (2011). "GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers." Genome Biology, 12:R41.
Beroukhim R, Mermel C, et al. (2010). "The landscape of somatic copy -number alteration across human cancers." Nature, 463:899-905.

· Beroukhim R, Getz G, et al. (2007). “Assessing the significance of chromosomal abberations in cancer: Methodology and application to glioma.” Proc Natl Acad Sci, 104:20007-20012.

虽然别人已经把软件做好了，但是刚开始使用，还是会遇到诸多问题，因此我记录一下我的一些经验。

模块的下载与安装

下载网址：http://portals.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=216&p=t
在Dupplemental Data的下方下载GISTIC 2.0.22 Source (.tar.gz)。
Installation Instruction可以在浏览器上看，也可以拷贝到本地文件，方便随时查询。
Follow这个Instruction进行安装——
首先拷贝压缩文件"GISTIC_2_0_X.tar.gz"到你想要的安装目录下。这里尽量不要安装到root权限才能操作的文件，推荐就在自己的用户目录下创建一个名为GISTIC2.0的文件夹，用下面命令进行拷贝和解压：
cp GISTIC_2_0_X.tar.gz <安装目录> (拷贝，也可以鼠标操作这一步)
tar zxf GISTIC_2_0_X.tar.gz （解压缩）
因为这个模块是基于MATLAB做出来的，所以需要安装相应的编译器（就是运行环境）MATLAB Component Runtime version7(MCR)。建议就安装在你已经想好的解压缩目录下，经过解压缩，目录下面已经自动生成了一个名为MATLAB Component Runtime的空文件夹，MCR的安装目录选择它就行了（当然你也可以选择其他目录，只是比较麻烦，说明里也有相应的介绍）。此处进行下面两步操作：
运用cd命令将终端目录切换至解压缩目录，比如我放在用户目录的GISTIC2.0下面，就在终端输入： cd ~/GISTIC2.0 即可
运行MCR安装包，在终端输入： ./MCRInstaller.bin
为了能够运行gistic模块，我们必须设置环境变量。注意，作者用的操作系统的系统shell工具是csh。如果你的系统使用的是csh命令，可以用作者提供的scripts设置：

FILL IN <mcr_root> HERE #####set mcr_root = <mcr_root> $thisdir/MATLAB_Component_Runtimeset mcr_root = /home/wsx/GISTIC2.0 $thisdir/MATLAB_Component_Runtimesetenv LD_LIBRARY_PATH $mcr_root/v714/runtime/glnxa64:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/os/glnxa64:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATHsetenv XAPPLRESDIR $mcr_root/v714/X11/app-defaults#####################################

如果你的系统与我一样是Ubuntu，或者是使用的bash命令，可以在 ~/.bashrc文件添加下列脚本：
export mcr_root=/home/wsx/GISTIC2.0/MATLAB_Component_Runtimeexport LD_LIBRARY_PATH=$mcr_root/v714/runtime/glnxa64:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/os/glnxa64:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATHexport XAPPLRESDIR=$mcr_root/v714/X11/app-defaults

注销重进，用export命令或者env命令查看环境变量是否添加成功。

然后输入当前目录终端下输入 ./run_gistic_example 命令，运行示例程序。
如果报错查不到环境变量——那就回头看看是否环境变量是否添加成功。
如果报错不能解析，请安装csh。命令是sudo apt-get install csh
如果说找不到共享库文件libXp.so.6，请下载后放到usr/lib下面（好像也能够直接安装）。我的Ubuntu上没有这个，所以在网上找寻了一番，下载地址是http://www.rpmfind.net/linux/rpm2html/search.php?query=libxp6&submit=Search+...
重新输入 ./run_gistic_example，大功告成，这个软件的配置到此也就基本结束了。更多高级操作，查看相关官方documentation。

最后，我们就可以看到示例文件运行的结果，各种生成的图片晃过眼睛，然后保存在(GISTIC2.0)安装目录的example_results文件夹下。