实验记录 | SpeedSeq安装

参考链接：https://github.com/hall-lab/speedseq

1。配置环境

下载安装包。
git clone --recursive https://github.com/hall-lab/speedseq
cd speedseq
make
报了一堆的错误。猜想可能是由于一些依赖的包是缺乏的。
参考链接：https://github.com/hall-lab/speedseq/blob/master/example/example_speedseq_install.sh
尝试按照示例代码一点点敲入，但是出现了报错。
由于我的系统是ubuntu，所以我使用apt-get代替示例代码中的yum。
sudo apt-get install make automake cmake gcc gcc-c++ git ncurses-devel zlib-devel

Reading package lists… Done
Building dependency tree
Reading state information… Done
E: Unable to locate package gcc-c+
E: Couldn’t find any package by regex ‘gcc-c+’
E: Unable to locate package ncurses-devel
E: Unable to locate package zlib-devel

再去查找出现了什么问题，我发现是由于ubuntu系统的改变，因此导致包的名字改变。
参考链接：https://blog.csdn.net/wang__rongwei/article/details/54846759
于是，现在去查找新的包的名字，无异于大海捞针。我决定从make报错中查找，我缺了什么包。

make align
make[1]: Entering directory ‘/home/zxx/workplace/speedseq’
make -C src/bwa
make[2]: Entering directory ‘/home/zxx/workplace/speedseq/src/bwa’
make[2]: Nothing to be done for ‘all’.
make[2]: Leaving directory ‘/home/zxx/workplace/speedseq/src/bwa’
cp src/bwa/bwa bin
cp src/sambamba bin
make -C src/samblaster
make[2]: Entering directory ‘/home/zxx/workplace/speedseq/src/samblaster’
make[2]: Nothing to be done for ‘SAMBLASTER’.
make[2]: Leaving directory ‘/home/zxx/workplace/speedseq/src/samblaster’
cp src/samblaster/samblaster bin
cd src/parallel; ./configure --prefix=/home/zxx/workplace/speedseq
checking for a BSD-compatible install… /usr/bin/install -c
checking whether build environment is sane… yes
checking for a thread-safe mkdir -p… /bin/mkdir -p
checking for gawk… no
checking for mawk… mawk
checking whether make sets $(MAKE)… yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
make -C src/parallel
make[2]: Entering directory ‘/home/zxx/workplace/speedseq/src/parallel’
make all-recursive
make[3]: Entering directory ‘/home/zxx/workplace/speedseq/src/parallel’
Making all in src
make[4]: Entering directory ‘/home/zxx/workplace/speedseq/src/parallel/src’
pod2man --release=‘20131022’ --center=‘parallel’
–section=1 ./parallel.pod > ./parallel.1
pod2man --release=‘20131022’ --center=‘parallel’
–section=1 ./sem.pod > ./sem.1
pod2man --release=‘20131022’ --center=‘parallel’
–section=1 ./sql > ./sql.1
pod2man --release=‘20131022’ --center=‘parallel’
–section=1 ./niceload.pod > ./niceload.1
pod2man --release=‘20131022’ --center=‘parallel’
–section=1 ./parallel_tutorial.pod > ./parallel_tutorial.1
pod2html ./parallel.pod > ./parallel.html
rm -f ./pod2htm*
pod2html ./parallel_tutorial.pod > ./parallel_tutorial.html
rm -f ./pod2htm*
pod2html ./sem.pod > ./sem.html
rm -f ./pod2htm*
pod2html ./sql > ./sql.html
rm -f ./pod2htm*
pod2html ./niceload.pod > ./niceload.html
rm -f ./pod2htm*
pod2texi --output=./parallel_tutorial.texi ./parallel_tutorial.pod || true
/bin/bash: pod2texi: command not found
pod2pdf --output-file ./parallel.pdf ./parallel.pod --title “GNU Parallel” || true
/bin/bash: pod2pdf: command not found
pod2pdf --output-file ./parallel_tutorial.pdf ./parallel_tutorial.pod --title “GNU Parallel Tutorial” || true
/bin/bash: pod2pdf: command not found
make[4]: Leaving directory ‘/home/zxx/workplace/speedseq/src/parallel/src’
make[4]: Entering directory ‘/home/zxx/workplace/speedseq/src/parallel’
make[4]: Leaving directory ‘/home/zxx/workplace/speedseq/src/parallel’
make[3]: Leaving directory ‘/home/zxx/workplace/speedseq/src/parallel’
make[2]: Leaving directory ‘/home/zxx/workplace/speedseq/src/parallel’
cp src/parallel/src/parallel bin
make[1]: Leaving directory ‘/home/zxx/workplace/speedseq’
make var
make[1]: Entering directory ‘/home/zxx/workplace/speedseq’
make -C src/freebayes
make[2]: Entering directory ‘/home/zxx/workplace/speedseq/src/freebayes’
wget -q http://hypervolu.me/freebayes/build/v0.9.21 &
cd src && make
make[3]: Entering directory ‘/home/zxx/workplace/speedseq/src/freebayes/src’
DETECTED_VERSION = v0.9.21
CURRENT_VERSION = v0.9.21
cd …/bamtools && mkdir -p build && cd build && cmake … && make
/bin/sh: 1: cmake: not found
Makefile:39: recipe for target ‘…/bamtools/lib/libbamtools.a’ failed
make[3]: *** […/bamtools/lib/libbamtools.a] Error 127
make[3]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes/src’
Makefile:2: recipe for target ‘all’ failed
make[2]: *** [all] Error 2
make[2]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes’
Makefile:116: recipe for target ‘freebayes’ failed
make[1]: *** [freebayes] Error 2
make[1]: Leaving directory ‘/home/zxx/workplace/speedseq’
Makefile:23: recipe for target ‘all’ failed
make: *** [all] Error 2

从这里也找不到线索，说缺啥。尝试失败。
那就接下来一个个的来安装先决环境。
sudo apt-get install libX11-devel libXpm-devel libXft-devel libXext-devel

E: Unable to locate package libX11-devel
E: Unable to locate package libXpm-devel
E: Unable to locate package libXft-devel
E: Unable to locate package libXext-devel

参考链接：https://blog.csdn.net/helaisun/article/details/79257697
之所以找不到包，是由于系统的版本不同，包的名字在更新的过程中也会产生变化。所以我现在的目标就是根据关键词去找，这些包在我的系统中所对应的名字是什么。然后安装。
主要的步骤如下：
首先，确定我的系统的版本。
sudo lsb_release -a

No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.5 LTS
Release: 18.04
Codename: bionic

我的系统的版本是bionic。
我就在https://packages.ubuntu.com/网站中，根据关键词，搜查与我的系统相对应的包的名字。
得到结果。

原名	现名
libX11-devel	libx11-dev
libXpm-devel	libxpm-dev
libXft-devel	libxft-dev
libXext-devel	libxext-dev

上述包全部安装成功。

同理，继续安装其他依赖的包。
sudo apt-get install make automake cmake gcc gcc-c++ git ncurses-devel zlib-devel

E: Unable to locate package gcc-c+
E: Couldn’t find any package by regex ‘gcc-c+’
E: Unable to locate package ncurses-devel
E: Unable to locate package zlib-devel

原名	现名
gcc-c+	暂无
ncurses-devel	lib64ncurses5-dev
zlib-devel	zlib1g-dev

sudo apt-get install make automake cmake gcc git lib64ncurses5-dev zlib1g-dev

安装成功！

sudo apt-get install python27 python27-devel python27-pip lapack lapack-devel blas blas-devel

E: Unable to locate package python27
E: Unable to locate package python27-devel
E: Unable to locate package python27-pip
E: Unable to locate package lapack
E: Unable to locate package lapack-devel
E: Unable to locate package blas
E: Unable to locate package blas-devel

原名	现名
python27	暂无
python27-devel	暂无
python27-pip	暂无
lapack	liblapack3
lapack-devel	liblapack-dev
blas	暂无
blas-devel	暂无

修改为：
sudo apt-get install liblapack3 liblapack-dev
安装成功！

2。安装root

下面开始安装root。
curl -OL ftp://root.cern.ch/root/root_v5.34.20.source.tar.gz

Command ‘curl’ not found, but can be installed with:
sudo apt install curl

所以接下来，看一下，curl是什么？

该命令设计用于在没有用户交互的情况下工作。
curl 是一个工具，用于传输来自服务器或者到服务器的数据。
可支持的协议有（DICT、FILE、FTP、FTPS、GOPHER、HTTP、HTTPS、IMAP、IMAPS、LDAP、LDAPS、POP3、POP3S、RTMP、RTSP、SCP、SFTP、SMTP、SMTPS、TELNET和TFTP）。
curl提供了大量有用的技巧，比如代理支持、用户身份验证、FTP上传、HTTP post、SSL连接、cookie、文件断点续传、Metalink等等。

下载curl指令。
sudo apt install curl

下载完成之后，重新运行指令。(12:02)
curl -OL ftp://root.cern.ch/root/root_v5.34.20.source.tar.gz

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- 0:02:15 --:–:-- 0curl: (7) Failed to connect to root.cern.ch port 21: Connection timed out

再次报错，ftp地址打不开，现在决定手动下载。
我们回溯到网站https://github.com/hall-lab/speedseq
发现有显示ROOT的网址为https://root.cern.ch/
我们在网址中找到与我们ubuntu系统一致的文件。

我们在选择下载的安装包时，源文件或二进制文件的区别是什么？
参考链接：https://blog.csdn.net/tiao321/article/details/109492581

所以，本次我们选择源文件进行安装。

https://github.com/hall-lab/speedseq/blob/master/example/example_speedseq_install.sh
https://root.cern.ch/releases/release-62400/

使用git指令下载：
git clone https://github.com/root-project/root.git
的确下载成功了，但是再进行下一步编译的时候，又遇到问题。
./configure
显示ROOT是由cmake编译的。
于是就:cmake root
结果文件夹下出现了一堆的文件，并不是我们想要的结果。

于是，选择手动下载，安装，解压缩。

出错。

CMakeFiles/XROOTD.dir/build.make:111: recipe for target ‘XROOTD-prefix/src/XROOTD-stamp/XROOTD-build’ failed
make[2]: *** [XROOTD-prefix/src/XROOTD-stamp/XROOTD-build] Error 1
CMakeFiles/Makefile2:288: recipe for target ‘CMakeFiles/XROOTD.dir/all’ failed
make[1]: *** [CMakeFiles/XROOTD.dir/all] Error 2
Makefile:151: recipe for target ‘all’ failed
make: *** [all] Error 2

(没有安装好root的情况下)
这个时候继续跑speedup的安装，那么：

src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:254: recipe for target ‘src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o’ failed
make[6]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1
make[6]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes/bamtools/build’
CMakeFiles/Makefile2:520: recipe for target ‘src/toolkit/CMakeFiles/bamtools_cmd.dir/all’ failed
make[5]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2
make[5]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes/bamtools/build’
Makefile:129: recipe for target ‘all’ failed
make[4]: *** [all] Error 2
make[4]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes/bamtools/build’
Makefile:39: recipe for target ‘…/bamtools/lib/libbamtools.a’ failed
make[3]: *** […/bamtools/lib/libbamtools.a] Error 2
make[3]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes/src’
Makefile:2: recipe for target ‘all’ failed
make[2]: *** [all] Error 2
make[2]: Leaving directory ‘/home/zxx/workplace/speedseq/src/freebayes’
Makefile:116: recipe for target ‘freebayes’ failed
make[1]: *** [freebayes] Error 2
make[1]: Leaving directory ‘/home/zxx/workplace/speedseq’
Makefile:23: recipe for target ‘all’ failed
make: *** [all] Error 2

我发现root有其他的安装方式。https://root.cern/install/
我有个想法，如果我不使用源文件，而是使用依赖于系统但不需要编译的二进制文件，是否可以更加方便一些？
好的，那我现在就去尝试。

重新开始。

下载事先编译（跳过前面非常复杂的编译过程）好的二进制的文件。
（1）安装好依赖的包。
sudo apt-get install dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev \ libxft-dev libxext-dev python libssl-dev
（2）下载对应版本的二进制文件。
链接：https://root.cern/download/root_v6.24.00.Linux-ubuntu18-x86_64-gcc7.5.tar.gz
（3）解压
tar -xzvf root_v6.24.00.Linux-ubuntu18-x86_64-gcc7.5.tar.gz
到这里，算是安装完成了root。
（4）将解压后的root文件存放到/usr/local
cd ..
sudo mv root /usr/local
（5）设置环境变量
echo "source /usr/local/root/bin/thisroot.sh" >> ~/.bashrc
source ~/.bashrc
（6）移除安装包
rm root_v5.34.20.source.tar.gz
（7）最后，检验是否安装成功。
在任意路径下输入root

---

| Welcome to ROOT 6.24/00 https://root.cern |
| © 1995-2021, The ROOT Team; conception: R. Brun, F. Rademakers |
| Built for linuxx8664gcc on Apr 14 2021, 14:33:50 |
| From tags/v6-24-00@v6-24-00 |
| With |
| Try ‘.help’, ‘.demo’, ‘.license’, ‘.credits’, ‘.quit’/’.q’ |
root [0]

---

如图所示，安装成功。

3。python2.7包

首先，安装pip，然后根据pip下载pysam，numpy，scipy三个包。

参考链接：https://blog.csdn.net/liumaolincycle/article/details/50547275

• 下载setuptools

wget --no-check-certificate https://bootstrap.pypa.io/ez_setup.py
sudo python ez_setup.py --insecure

• 下载pip安装包，解压
  参考链接：https://pypi.org/project/pip/#files
  tar -zxvf pip-21.1.1.tar.gz
• 安装pip
  cd pip-21.1.1/
sudo python setup.py install
• pip安装完成之后，使用pip安装包pysam，numpy，scipy
  pip install pysam numpy scipy

Collecting numpy
Downloading numpy-1.20.2-cp39-cp39-manylinux2010_x86_64.whl (15.4 MB)
|████████████████████████████████| 15.4 MB 12.1 MB/s
Collecting pysam
Downloading pysam-0.16.0.1.tar.gz (3.6 MB)
|████████████████████████████████| 3.6 MB 11.0 MB/s
Collecting scipy
Downloading scipy-1.6.3-cp39-cp39-manylinux1_x86_64.whl (27.3 MB)
|████████████████████████████████| 27.3 MB 11.3 MB/s
Building wheels for collected packages: pysam
Building wheel for pysam (setup.py) … done
Created wheel for pysam: filename=pysam-0.16.0.1-cp39-cp39-linux_x86_64.whl size=2992268 sha256=aaa602cfe1592e65b556de3ae2b316b7047f873a85d4abadeba07dc0cb78aba4
Stored in directory: /home/zxx/.cache/pip/wheels/fb/96/5b/d62b12ccae437c41f0368bca424aa34b6d3f9fef4a38640edc
Successfully built pysam
Installing collected packages: numpy, scipy, pysam
Successfully installed numpy-1.20.2 pysam-0.16.0.1 scipy-1.6.3

安装完成。

4。加载Speedup

仍然是莫名原因出错。