* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * PAA(蛋白质阵列分析仪)自述文件* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | 1。PAA -包安装| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PAA安装推荐的方法是在R控制台输入下面描述的命令:> #如果你安装一个Bioconductor包第一次源(“//www.anjoumacpherson.com/biocLite.R”) > > # >其他图书馆(BiocInstaller) > biocLite (PAA,依赖= TRUE)这将安装PAA包括所有依赖项。- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | 2。随机丛林安装| - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PAA外部依赖,需要提供完整的功能。这个外部的依赖是免费的c++软件随机丛林(RJ),可以从http://www.randomjungle.de/下载。PAA没有RJ将可用。然而,它需要这个包随机丛林的递归特性消除(RJ-RFE)提供的函数selectFeatures ()。请按照下面的说明对你的操作系统安装RJ正确地在您的机器上。Windows 2.1 - - - - - - - - - - - - (a)去“http://www.randomjungle.de/”。(b)下载并解压缩适当Windows档案(32位0 r 64位)包含预编译RJ二进制文件。 (c) Make RJ available for PAA by adding the path to the binaries (e.g., "C:\rjungle\programs\rjungle\bin") to the PATH variable. (d) As a quick test for a successful installation type "rjungle --version" or "rjungle --help" in the Windows Command Prompt. 2.2 Linux --------- (a) Go to "http://www.randomjungle.de/". (b) Download and extract the appropriate Linux tarball (32 bit 0r 64 bit) containing precompiled RJ binaries. (c) Copy the binaries "rjungle" and "rjungle_static" to "/usr/local/bin" to make RJ available for PAA. (d) As a quick test for a successful installation type "rjungle --version" or "rjungle --help" in the Linux console. 2.3 Mac ------- Unfortunately in the medium term there will be no Mac binaries available on "http://www.randomjungle.de/". But it is planned in the long term (according to the RJ developers). As a consequence RJ has to be compiled from the source code. (a) Install gcc (download from "https://gcc.gnu.org/") via "configure", "make" and "make install". (b) Download boost(e.g., "boost_1_55_0.tar.bz2" from "http://www.boost.org/") and install it via "tar --bzip2 -xf /path/to/boost_1_55_0.tar.bz2". (c) Install gsl (download from "http://www.gnu.org/software/gsl/") via "configure", "make" and "make install". (d) Download "randomjungle-master.zip" from "https://github.com/insilico/randomjungle" via the "Download ZIP" button. (e) Unzip "randomjungle-master.zip" then cd into the new randomjungle-master order and "make clean". (f) "./configure CXX='/usr/local/bin/gcc' CXXFLAGS='-fpermissive -lstdc++' --with-boost='/usr/local/boost_1_55_0'" (-lstdc++ is needed to solve possible linking errors). (g) "make". (h) "make install". (i) By default the binaries "rjungle" and "rjungle_static" will be installed in "/usr/local/bin" and should be available for PAA immediately. (j) As a quick test for a successful installation type "rjungle --version" or "rjungle --help" in the Mac terminal.