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perl/linux/测序分析

ABySS非root权限安装

ABySS:

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

ABySS是一个能并行的,双端测序短序列组装软件(单端也行),但线程版本可用于之多100M基因组的拼接,并行版本采用MPI并行算法,能拼接比100M更大的基因组。组装转录组数据可用Trans-ABySS. 据我简单调研,ABySS 在病毒基因组拼接中使用广泛[1,2],所以我在这里安装ABySS的目的就是用来组装一个病毒基因组。

安装:

安装ABySS需要以下依赖包:

ABySS需要支持OpenMP的C++编译器如gcc 4.2或以上;另外当使用Boost 1.51.0 or 1.52.0版本时,ABySS编译会出现报错,后续版本没这个bug.

下面是非root权限安装步骤:

1.安装gcc

首先看看自己有没有安装gcc及gcc版本: gcc -v; 由于我的版本4.8.1,所以我就不需要安装,下面贴出其他站点的一个安装步骤以供参考:

编译安装gcc之前需要先安装三个必须的软件,分别下载之:

GMP:

wget ftp://ftp.gmplib.org/pub/gmp-5.0.1/gmp-5.0.1.tar.bz2
解压:tar jxvf gmp-5.0.1.tar.bz2
进入目录:cd gmp-5.0.1
配置:./configure –prefix=$HOME
编译:make
安装:make install

(下面的过程比较相似,只写出配置步骤)

MFPR:

wget http://www.mpfr.org/mpfr-current/mpfr-3.0.0.tar.bz2
./configure –prefix=$HOME –with-gmp=$HOME

MPC:

wget http://www.multiprecision.org/mpc/download/mpc-0.8.2.tar.gz
./configure –prefix=$HOME

在这里我们在配置的时候将安装目录统一指定为$HOME,将程序执行文件,库文件及头文件全部安装在自己的目录下,呵呵,因为没有root嘛

下载新版gcc:

wget http://gcc-uk.internet.bs/releases/gcc-4.5.1/gcc-4.5.1.tar.bz2

./configure –prefix=$HOME –with-gmp=$HOME –with-mpfr=$HOME –with-mpc=$HOME

这样新版的gcc就安装到了我们的home目录,为了默认使用新的gcc修改自己的配置文件例如.bash_profile或.bashrc

2. boost 安装

下载,直接解压即可

wget http://downloads.sourceforge.net/project/boost/boost/1.56.0/boost_1_56_0.tar.bz2

tar jxf boost_1_56_0.tar.bz2  (解压好得到boost_1_56_0文件夹,此时就可以了)

mv boost_1_56_0 /share/workdir/yangl/soft (说明一下我的家目录不是/home/yangl,而是/share/workdir/yangl,我的软件全部装在/share/workdir/yangl/soft ,所以我把它已到我的软件安装目录下

3. sparsehash 安装

下载地址:https://github.com/sparsehash/sparsehash(sparsehash: version 2.0.3)
下载方法:进入下载地址 -> 页面右侧找到 Download zip 按钮 -> 下载

 

解压: gunzipsparsehash-master.zip
cd sparsehash-master
./configure –prefix=/share/workdir/yangl/soft/sparsehash
make
make install

4. Open MPI 安装

下载地址:http://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.1.tar.bz2

tar xf openmpi-X.Y.Z.tar.gz
cd openmpi-X.Y.Z
./configure –prefix=/share/workdir/yangl/soft/openmpi
make all install

安装好后准备安装ABySS,再ABySS安装的make这一步时报错:/usr/bin/ld: cannot find -lsqlite3 ,经过研究发现需要安装sqlite

5. sqlite安装

下载地址:http://www.sqlite.org/2015/sqlite-autoconf-3090200.tar.gz  (version 3.9.2

tar -xvf sqlite-autoconf-3090200.tar
cd sqlite-autoconf-3090200
./configure –prefix=/share/workdir/yangl/soft/sqlite
make
make install

至此所有依赖包安装完成,全部安装在目录:/share/workdir/yangl/soft 下

6. ABySS安装

下载地址:https://github.com/bcgsc/abyss/releases/download/1.9.0/abyss-1.9.0.tar.gz

tar -zxvf abyss-1.9.0.tar.gz
./configure –prefix=/share/workdir/yangl/soft/abyss –with-boost=/share/workdir/yangl/soft/boost_1_56_0 –with-mpi=/share/workdir/yangl/soft/openmpi CPPFLAGS=-I/share/workdir/yangl/soft/sparsehash/include –enable-maxk=96 –with-sqlite=/share/workdir/yangl/soft/sqlite
make
make install

注意:配置时 CPPFLAGS=-I/share/workdir/yangl/soft/sparsehash/include: sparsehash需要执行它的include文件夹

[1] Carrera, J. P., et al. (2015). “Mercadeo Virus: A Novel Mosquito-Specific Flavivirus from Panama.” Am J Trop Med Hyg 93(5): 1014-1019.

[2] Gandar, F., et al. (2015). “The Genome of a Tortoise Herpesvirus (Testudinid Herpesvirus 3) Has a Novel Structure and Contains a Large Region That Is Not Required for Replication In Vitro or Virulence In Vivo.” Journal of Virology 89(22): 11438-11456.

 

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  1. #0

    amoxil

    TiSrqxh2n5年前 (2016-02-29)回复