中科院超级计算青岛分中心Mira安装手册

安装目录: 
/public/home/ningjuan/bin/mira
软件介绍: 

MIRA is the swiss army knife of sequence assembly that I've used and developed during the past 16 years to get assembly jobs I work on done efficiently - and especially accurately. That is, without me actually putting too much manual work into it.

Over time, other labs and sequencing providers have found mira useful for assembly of extremely 'unfriendly' projects containing lots of repetitive sequences. As always, your mileage may vary.

使用用户: 

王敏晓,生态室

联系方式: 82898925; 82898862 wangminxiao@qdio.ac.cn
 

安装步骤: 

安装mira-3.4.0.1详细步骤:

gcc (GCC) 4.1.2 20070115 (SUSE Linux)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 

 

Download necessary files.

Commands are written in different font.

 

Googlemail is somewhat limited in its abilities to format code :-)

Hopefully everthing is "readable".

 

## whatever path is approbiate

cd /public/home/ningjuan/bin/

 

## expat

tar zxvf expat-2.0.1.tar.gz

cd expat-2.0.1

./configure --prefix=/public/home/ningjuan/bin/expat

make && make install

 

## flex

cd /public/home/ningjuan/bin/

tar zxvf flex-2.5.35.tar.gz

cd flex-2.5.35

./configure --prefix=/public/home/ningjuan/bin/flex

make && make install

cd /public/home/ningjuan/bin/flex/bin

ln -s flex flex++

export PATH=/public/home/ningjuan/bin//flex/bin:$PATH

 

## boost

cd /public/home/ningjuan/bin/

tar zxvf boost_1_48_0.tar.gz

cd boost_1_48_0

./bootstrap.sh --prefix=/public/home/ningjuan/bin//boost

./b2 install

 

## libunwind and google-perftools

cd /public/home/ningjuan/bin/

tar zxvf libunwind-1.0.1-tar.gz

cd libunwind-1.0.1

./configure --prefix=/public/home/ningjuan/bin/libunwind

make && make install

 

cd /public/home/ningjuan/bin/

tar zxvf gperftools-2.0.tar.gz

cd gperftools-2.0

export LDFLAGS="-L/public/home/ningjuan/bin/libunwind/lib"

export CPPFLAGS="-I/public/home/ningjuan/bin/libunwind/include"

./configure --prefix=/public/home/ningjuan/bin//gperftools

make && make install

 

## mira itself

export CXXFLAGS="-I/public/home/ningjuan/bin//flex/include"

 

cd /public/home/ningjuan/bin/
tar zxvf mira-3.4.0.1.tar.gz

cd mira-3.4.0.1

./configure --prefix=/public/home/ningjuan/bin/mira \

--with-boost=/public/home/ningjuan/bin/boost \

--with-expat=/public/home/ningjuan/bin/expat \

--with-tcmalloc-dir=/public/home/ningjuan/bin/google-perftools/lib \

--enable-mirastatic

或FLEX=/public/home/ningjuan/bin/flex/bin/flex ./configure --prefix=/public/home/ningjuan/bin/mira --with-boost=/public/home/ningjuan/bin/boost/ --with-boost-libdir=/public/home/ningjuan/bin/boost/lib/ --with-tcmalloc-dir=/public/home/ningjuan/bin/gperftools/lib --enable-64=yes --enable-mirastatic --with-expat=/public/home/ningjuan/bin/expat
 

[...]

--------------------------------------------------------------------------------

                       Summary of MIRA configuration

--------------------------------------------------------------------------------

 

Building version .................................

3.4.0.1_prod_linux-gnu_x86_64_static

Production or development version?................ production

 

We are building on ............................... Linux

CPU supports 64 bit? ......... ................... yes

Compiler ......................................... gcc

Compiler optimisation flags used ................. -O3 -funroll-loops

Do we compile in 64 bit? ......................... yes

Building completely static? ...................... yes

BOOST expected to compile and link?............... yes

Linking with TCmalloc library?.................... yes

 

Can MIRA be built on this system? ................ yes

 

Using CFLAGS   :   -I/public/home/ningjuan/bin/mira/include -O3 -funroll-loops

-I/public/home/ningjuan/bin/expat/include

Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64

-I/public/home/ningjuan/bin/flex/include  -I/public/home/ningjuan/bin/mira/include -O3

-funroll-loops -I/public/home/ningjuan/bin/expat/include -pthread

-I/public/home/ningjuan/bin/boost/include

Using LDFLAGS  : -L/public/home/ningjuan/bin/libunwind/lib

-L/public/home/ningjuan/bin/mira/lib  -L/public/home/ningjuan/bin/boost/lib

-lboost_thread -lboost_regex

 

Looks good, we do not expect compilation problems.

--------------------------------------------------------------------------------

 

 

make && make install

 

cd ../../mira/bin

./mira

This is MIRA V3.4.0.1 (production version).