augustus:一基因预测软件;
Docker:应用容器引擎,可实现虚拟机。
本机系统:CentOS7
git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus
make augustus
## 报错如下:
mkdir -p bin
cd src && make
make[1]: Entering directory `/home/yl/software/Augustus/src'
g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc
In file included from randseqaccess.cc:10:0:
../include/randseqaccess.hh:21:29: fatal error: mysql++/mysql++.h: No such file or directory
#include <mysql++/mysql++.h>
^
compilation terminated.
make[1]: *** [randseqaccess.o] Error 1
make[1]: Leaving directory `/home/yl/software/Augustus/src'
make: *** [augustus] Error 2
直接下载的二进制文件和conda安装都无法正常使用。
~/software/augustus-3.4.0/bin
$ ~/software/augustus-3.4.0/bin/augustus
augustus: error while loading shared libraries: libboost_iostreams.so.1.71.0: cannot open shared object file: No such file or directory
参考问答页面:https://github.com/Gaius-Augustus/Augustus/issues/156.
该问题可能是Centos的gcc版本及 Application Binary Interface (ABI) 引起。
需要root
yum upgrade
yum install docker
[root@localhost software]# docker -v
Docker version 1.13.1, build 7d71120/1.13.1
# 启动
systemctl start docker
# 安装Augustus
git clone https://github.com/Gaius-Augustus/Augustus.git
cd Augustus
docker build -t augustus .
并不顺利~
出现该问题的原因有很多,更新及换源可能解决
直接改Dockerfile
# Install required packages
RUN apt-get clean
RUN apt-get -y update
此两行改成以下样式,使用清华镜像:
# Install required packages
RUN sed -i s:/archive.ubuntu.com:/mirrors.tuna.tsinghua.edu.cn/ubuntu:g /etc/apt/sources.list
RUN apt-get clean
RUN apt-get -y update --fix-missing
再次执行docker build -t augustus .
等待片刻即可。
非root用户需要创建docker用户组,添加非root用户进docker组,重启docker即可。
[yl@localhost ~]$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
augustus latest 8a9548d0bcfc About an hour ago 2.53 GB
...
[yl@localhost ~]$ docker run -i augustus augustus --version # -i传入参数
AUGUSTUS (3.4.0) is a gene prediction tool.
Sources and documentation at https://github.com/Gaius-Augustus/Augustus
可正常使用。
https://blog.csdn.net/ctwy291314/article/details/104967075.
https://github.com/Gaius-Augustus/Augustus/issues/156