安装Amos
The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler. Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.
Amos是纯于比较难安装那种，因为依赖关系比较复杂。
首先编译需要qt4-dev和boost graph toolkit：
sudo apt-get install libqt4-dev
sudo apt-get install libboost-graph-dev
再者是perl模块：
sudo cpan -i DBI
sudo cpan -i Statistics::Descriptive
还有一些第三方的软件MUMmer和BLAT，MUMmer可以通过apt安装：
sudo apt-get install mummer
但BLAT则需要自己编译：
wget -c https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip
unzip blatSrc35.zip
cd blatSrc
mkdir -p ~/bin/x86_64
make 'MACHTYPE = x86_64'
sudo mkdir /opt/blat
sudo cp ~/bin/x86_64/* /opt/blat/
安装好再把/opt/blat加到$PATH中。 解决了各种依赖关系就可以准备安装：
./configure --prefix=/opt/amos
make
g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -g -O2 -MT find-tandem.o -MD -MP -MF .deps/find-tandem.Tpo -c -o find-tandem.o find-tandem.cc
find-tandem.cc: In function ‘int main(int, char**)’:
find-tandem.cc:245:3: error: ‘optarg’ was not declared in this scope
optarg = NULL;
^
find-tandem.cc:247:63: error: ‘getopt’ was not declared in this scope
while (!errflg && ((ch = getopt (argc, argv, "f:u:l:x:m:k:h")) != EOF))
^
find-tandem.cc:260:55: error: ‘optopt’ was not declared in this scope
fprintf (stderr, "Unrecognized option -%c\n", optopt);
^
Makefile:918: recipe for target 'find-tandem.o' failed
make[3]: *** [find-tandem.o] Error 1
make[3]: Leaving directory '/home/labuser/ygc/amos-3.1.0/src/Align'
Makefile:325: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/labuser/ygc/amos-3.1.0/src'
Makefile:306: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/labuser/ygc/amos-3.1.0'
Makefile:244: recipe for target 'all' failed
make: *** [all] Error 2
结果还是报错，但原因非常明显，就是没有定义getopt，于是修改find-tandem.cc
mg src/Align/find-tandem.cc
加入：
#include <getopt.h>
再次make，则整个世界清净了
make
sudo make install
安装后把/opt/amos/bin加入到$PATH中去即可。
上面是我在2015年安装Amos的过程，实验室的机器用的Ubuntu，过程还挺繁琐，因为依赖还蛮多的，对于现在用Arch的我来说，就再简单不过了，因为Arch的AUR上几乎啥软件都有。
aur/amos 3.1.0-3 (+2 0.00%)
A modular, open source whole-genome assembler
要安装Amos，只需要一条指令：
yay -S amos
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