实验记录 | Mutect的安装

参考链接：https://github.com/broadinstitute/mutect
安装Mutect之前，需要先安装java 1.7以及Maven 3.0+。

1。 环境配置

首先检验一下系统中的java版本。
java -version

java version “1.8.0_181”

下面，开始检索安装Maven。
安装参考链接：https://blog.csdn.net/qq_29695701/article/details/90705181

从官网下载Maven,下载地址：https://maven.apache.org/download.cgi
下载之后，解压。
unzip apache-maven-3.8.1-bin.zip
将解压后的文件移动到系统文件夹中
创建文件夹存放。
sudo mkdir /usr/local/maven
sudo mv apache-maven-3.8.1 /usr/local/maven/
接着，配置环境变量。
echo "MAVEN_HOME=/usr/local/maven/apache-maven-3.8.1" >> ~/.bashrc
echo "PATH=\${PATH}:\${MAVEN_HOME}/bin" >> ~/.bashrc
echo "export PATH" >> ~/.bashrc
source ~/.bashrc
配置好环境变量之后，安装完成。
检验是否安装成功：
mvn -v

Apache Maven 3.8.1 (05c21c65bdfed0f71a2f2ada8b84da59348c4c5d)
Maven home: /usr/local/maven/apache-maven-3.8.1
Java version: 1.8.0_181, vendor: Oracle Corporation, runtime: /usr/lib/jvm/jdk1.8.0_181/jre
Default locale: en_US, platform encoding: UTF-8
OS name: “linux”, version: “5.4.0-72-generic”, arch: “amd64”, family: “unix”

即是安装完成。

2。安装mutect

首先在workplace创建文件夹。
sudo mkdir mutect-src
cd mutect-src/
按照官网教程一步步跑下去，发现报错。
git clone git@github.com:broadinstitute/mutect.git
具体的报错内容如下：

fatal: could not create work tree dir ‘mutect’: Permission denied

简而言之，就是没有权限写入。
我去检索一下其他的教程。
找到解疑的教程：https://blog.csdn.net/one_girl/article/details/82887067
按照过程继续操作。
修改文件夹的权限。
cd ../
sudo chmod o+w mutect-src/

修改完成之后，继续进入文件夹中。
继续git clone，但是报了另外的错。

The authenticity of host ‘github.com (13.250.177.223)’ can’t be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added ‘github.com,13.250.177.223’ (RSA) to the list of known hosts.
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.

参考教程https://blog.csdn.net/yushuangping/article/details/84240863，尝试添加key。

一开始按照教程，添加的key，并不好用，系统显示太弱。于是参考github官网的流程，再结合上述笔记，最终成功完成。
官网教程：https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent

基本步骤：
ssh-keygen -t rsa -b 4096 -C "2456392738@qq.com"
注释：2456392738@qq.com是我的github的账户，所以同样的替换成你的账号即可。
输入之后，会出现：

Generating public/private rsa key pair.

Enter file in which to save the key (/home/zxx/.ssh/id_rsa): /home/zxx/.ssh/id_rsa already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/zxx/.ssh/id_rsa.
Your public key has been saved in /home/zxx/.ssh/id_rsa.pub.
The key fingerprint is:
SHA256:0P9FLeLAzZ5XQ8T4dbeUZsuA7wDu2Xt+V9CVcRD8a0I 2456392738@qq.com
The key’s randomart image is:
±–[RSA 4096]----+
| …**=|
| . o + ooO*|
| . o + = X+X|
| . o = E.B+|
| S + B o…|
| o o = o.|
| o o .|
| . . …|
| o… .|
±—[SHA256]-----+

显示如上，就表示添加成功。其中需要注意的是，我的操作将key保存到/home/zxx/.ssh/id_rsa.pub文件夹中，以后会用到。
eval "$(ssh-agent -s)"
ssh-add /home/zxx/.ssh/id_rsa
这里的地址就算上述我们提到的。
到这里，key基本上获取完成了。接着要做的事情就是，将key拷贝下来。
cat /home/zxx/.ssh/id_rsa.pub
界面上显示了key的一长串字符。

ssh-rsa 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 2456392738@qq.com

接着，就是将key添加到自己的github账户中。
添加过程可参考作者https://blog.csdn.net/yushuangping/article/details/84240863

之后，重试clone指令。
git clone git@github.com:broadinstitute/mutect.git

Cloning into ‘mutect’…
Warning: Permanently added the RSA host key for IP address ‘52.74.223.119’ to the list of known hosts.
remote: Enumerating objects: 1157, done.
remote: Total 1157 (delta 0), reused 0 (delta 0), pack-reused 1157
Receiving objects: 100% (1157/1157), 73.54 MiB | 1.03 MiB/s, done.
Resolving deltas: 100% (336/336), done.

显示没有报错，clone成功。那么，接下来继续推进下一步。
参考官网：https://github.com/broadinstitute/mutect
git clone git@github.com:broadgsa/gatk-protected.git

Cloning into ‘gatk-protected’…
remote: Enumerating objects: 205181, done.
remote: Total 205181 (delta 0), reused 0 (delta 0), pack-reused 205181
Receiving objects: 100% (205181/205181), 252.00 MiB | 489.00 KiB/s, done.
Resolving deltas: 100% (109673/109673), done.

继续运行，以为一切万事大吉的时候，又报错了。
git clone git@github.com:broadgsa/gatk-protected.git
cd gatk-protected
git reset --hard 3.1
mvn -Ddisable.queue install

[ERROR] Failed to execute goal com.pyx4j:maven-junction-plugin:1.0.3:link (link-public-testdata) on project sting-aggregator: Execution link-public-testdata of goal com.pyx4j:maven-junction-plugin:1.0.3:link failed: Plugin com.pyx4j:maven-junction-plugin:1.0.3 or one of its dependencies could not be resolved: Failed to collect dependencies at com.pyx4j:maven-junction-plugin:jar:1.0.3 -> sysinternals:junction:exe:1.04: Failed to read artifact descriptor for sysinternals:junction:exe:1.04: Could not transfer artifact sysinternals:junction:pom:1.04 from/to maven-default-http-blocker (http://0.0.0.0/): Blocked mirror for repositories: [pyx4me-web (http://www.pyx4me.com/maven2, default, releases)] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginResolutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :sting-aggregator

目前猜测是缺少Aggregator这个插件，于是现在尝试配置。

跳过，运行下一步。
cd ../mutect
mvn verify
继续报错。

[ERROR] Failed to execute goal on project mutect: Could not resolve dependencies for project org.broadinstitute.cga:mutect:jar:1.1.7: Failed to collect dependencies at org.broadinstitute.sting:gatk-protected:jar:3.1: Failed to read artifact descriptor for org.broadinstitute.sting:gatk-protected:jar:3.1: Could not transfer artifact org.broadinstitute.sting:gatk-protected:pom:3.1 from/to sting.public.repo.local (file:…/…/gatk-protected/public/repo): Repository path …/…/gatk-protected/public/repo does not exist, and cannot be created. -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

暂时，安装到这里，等有心情回来继续安装。