生物信息软件安装（不定时更新）
(以本地电脑wsl子系统的unbantu为例)
软件安装
- anaconda安装与配置
- 下载Anaconda 2.7 for Linux https://www.anaconda.com/download/
- 在下载目录下输入
bash Anaconda2-2.2.1-Linux-x86_64.sh #安装Anaconda
- 点yes往下后，输入查看是否安装成功
python -V #查看Python 版本
结果为
Python 2.7.x :: Anaconda x.x.x (x86_64)
- 更新环境配置
echo export PATH=$HOME/anaconda3/bin:$PATH >> ~/.bashrc
source ~/.bashrc #更新
- 增加源（channels）
conda config --add channels bioconda
conda config --add channels conda-forge
# 设置搜索时显示通道地址
conda config --set show_channel_urls yes
现在anconda下载好了
2.faToTwoBit安装 （将fasta格式改为 .2bit格式）
conda install ucsc-fatotwobit # 安装包
conda update ucsc-fatotwobit # 更新包
3.安装bedtools
sudo apt-get install bedtools
4.安装MAFFT
conda install MAFFT
5.安装BESST
pip install BESST
6.安装minimap2
conda install minimap2
7.安装BBmap
conda install BBmap
8.安装seqkit
conda install -c bioconda seqkit
9.安装Gblocks
~~~
wget http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z # 下载安装包
sudo yum install -y ncompress # 安装
tar Zxf Gblocks_Linux64_0.91b.tar.Z -C /opt/biosoft/ # 解压
echo 'PATH=$PATH:/home/train/biosoft/Gblocks_0.91b/' >> ~/.bashrc # 配置环境
source ~/.bashrc
~~~
10.安装tree命令
sudo yum -y install tree
可是中间出现了 Yum：[Errno 5] [Errno 2] No such file or directory
这是由于系统之前升级过python，原来版本是2.7，升级python3后，yum 调用python找不到2.7的版本了
有两个配置文件需要修改
将·#! /usr/bin/env python2 # 改为
#! /usr/bin/env python2.7
vim /usr/libexec/urlgrabber-ext-down
将·#! /usr/bin/env python2 # 改为
#! /usr/bin/env python2.7
然后直接sudo yum -y install tree
11.序列拼接软件stampy的安装
需要gsl依赖，请看下文。
进入官网，填写邮箱，等压缩包
解压缩，
然后make
异常，出现了/usr/bin/ld: cannot find -lpython2.7
解决方法
sudo ln -s /home/train/anaconda3/envs/fcx/lib/python2.7/config/libpython2.7.a /usr/lib/#创建软连
echo 'PATH=$PATH:/home/train/Biosoft/stampy-1.0.21/' >> ~/.bashrc#配置环境
source ~/.bashrc
结果执行时又出现了权限不允许
(fcx2.7) [train@train stampy-1.0.32]$ ./stampy.py
-bash: ./stampy.py: Permission denied
使用sudo命令，还是不行
(fcx2.7) [train@train stampy-1.0.32]$ sudo ./stampy.py
[sudo] password for train:
sudo: ./stampy.py: command not found
后来想了想，用python查看是否安装正确
(fcx2.7) [train@train stampy-1.0.32]$ python stampy.py
stampy v1.0.32 (r3761), <gerton.lunter@well.ox.ac.uk>
Usage: stampy.py [options] [.fa files]
....
可见安装正确，改一下权限就行
chmod +x stampy.py
执行./stampy.py
stampy v1.0.32 (r3761), <gerton.lunter@well.ox.ac.uk>
12 zlib库安装
ubantu版
sudo apt-get install ruby
sudo apt-get install zlib1g
sudo apt-get install zlib1g.dev
- 安装megahit
git clone https://github.com/voutcn/megahit.git
cd megahit
make
./megahit -1 pe_1.fq.gz -2 pe_2.fq.gz -o megahit_out
make 时候出错，
/usr/bin/ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
make: *** [megahit_asm_core] Error 1
可能是因为系统没有安装 std
sudo yum search stdc
sudo yum install libstdc++-devel.x86_64 libstdc++.x86_64 compat-libstdc++-33.x86_64 libstdc++-static.x86_64
14.samtools
OS : centos 7
pbzip2: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
刚开始，以为此软件没有安装，于是yum install bzip2-libs 。安装之后，依然报错。后来使用find / -name libbz2.so查找文件位置，发现都在/usr/lib64/目录下，然后在此目录中，
做一个软链接libbz2.so.1.0，指向已经有的libbz2.so.1.0.6
[root@username run]# cd /usr/lib64/
[root@username lib64]# ls -alhtr | grep libbz2.so.1
-rwxr-xr-x. 1 root root 67K Nov 20 2015 libbz2.so.1.0.6
lrwxrwxrwx. 1 root root 15 Aug 21 11:59 libbz2.so.1 -> libbz2.so.1.0.6
lrwxrwxrwx. 1 root root 11 Sep 8 12:17 libbz2.so -> libbz2.so.1
[root@username lib64]# ln -s libbz2.so.1.0.6 libbz2.so.1.0
[root@username lib64]# ls -alhtr | grep libbz2.so.1
-rwxr-xr-x. 1 root root 67K Nov 20 2015 libbz2.so.1.0.6
lrwxrwxrwx. 1 root root 15 Aug 21 11:59 libbz2.so.1 -> libbz2.so.1.0.6
lrwxrwxrwx. 1 root root 11 Sep 8 12:17 libbz2.so -> libbz2.so.1
lrwxrwxrwx. 1 root root 15 Nov 8 01:34 libbz2.so.1.0 -> libbz2.so.1.0.6
15.lighter安装
conda install lighter --channel bioconda
16.fastp安装
conda install -c bioconda fastp
17.minia安装
# get a local copy of minia source code
git clone --recursive https://github.com/GATB/minia.git
# compile the code an run a simple test on your computer
cd minia
sh INSTALL
没有安装成功
## Download and install Minia
# http://minia.genouest.org/
cd ~/biosoft
wget https://github.com/GATB/minia/releases/download/v2.0.7/minia-v2.0.7-bin-Linux.tar.gz
tar -zxvf minia-v2.0.7-bin-Linux.tar.gz
echo 'PATH=$PATH:/home/biosoft/minia-v2.0.7-bin-Linux/bin/' >> ~/.bashrc
source ~/.bashrc
18.fastqc安装
conda install fastqc
19.gapcloser安装
conda install soapdenovo2-gapcloser
