个人PC Centos7下生物学软件安装记录

1. gcc

yum install -y gcc

2. mysql

yum install mysql
yum install mysql-devel

centos7没有mysql-server的yum源，因此需手动配置

wget http://dev.mysql.com/get/mysql-community-release-el7-5.noarch.rpm
rpm -ivh mysql-community-release-el7-5.noarch.rpm
yum install mysql-community-server

启动mysql服务

service mysqld restart

初次安装mysql，root账户没有密码

mysql -u root
mysql> show databases；

设置密码

mysql> set password for 'root'@'localhost' =password('password');

创建用户

mysql> GRANT SELECT ON *.* TO 'pasa'@'%' IDENTIFIED BY '123456';
mysql> GRANT ALL ON *.* TO 'slbai'@'%' IDENTIFIED BY '123456';
mysql> FLUSH PRIVILEGES;

配置mysql

mysql配置文件为/etc/my.cnf
最后加上编码配置

[mysql]
default-character-set =utf8

3. blatSrc

wget http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip
unzip blatSrc35.zip
cd blatSrc
MACHTYP=x86_64
export MACHTYPE
mkdir -p ~/bin/x86_64
make

若make报错为：

cd lib && make
make[1]: Entering directory /home/slbai/program/blatSrc/lib'
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o pngwrite.o -c pngwrite.c
pngwrite.c:7:87: fatal error: png.h: No such file or directory
#include "png.h" // MUST come before common.h, due to setjmp checking in pngconf.h
^
compilation terminated.
make[1]: *** [pngwrite.o] Error 1
make[1]: Leaving directory/home/slbai/program/blatSrc/lib’
make: * [all] Error 2

是由于缺少libpng-devel导致的，安装后即可make成功

yum install libpng-dev

4. perl模块DBD::mysql

yum install cpan
yum install gd-devel
# cpan
cpan[1]> install DBD::mysql
cpan[1]> install GD

5. GMAP

tar zxvf gmap-gsnap-2016-11-07.tar.gz 
cd gmap-2016-11-07/
./configure --prefix=/home/slbai/program/gmap-2016-11-07
make
make install
cd bin; ./gmap

6. FASTA

tar zxvf fasta36-linux64.tar.gz
cd fasta-36.3.8e/
cd src/
make -f ../make/Makefile.linux_sse2 all
cd ../bin/
./fasta36

7. PASA

yum install -y gcc-c++-4.8.5-11.el7.x86_64
tar zxvf PASApipeline-2.0.2.tar.gz
cd PASApipeline-2.0.2/
make