Ubuntu下安装并配置IGV(两个巨坑！)

作者: 一只烟酒僧 | 来源:发表于2020-05-23 16:55 被阅读0次

Ubuntu下安装并配置IGV(两个巨坑！)
Ubuntu anaconda 配置 Jupyter Lab
关于RabbitMQ安装遇到的问题
Ubuntu安装IGV
Ubuntu 下开发环境搭建
Ubuntu安装配置Redis
MacOS 安装opencv后，配置/测试opencv的巨坑
Ubuntu下配置Nginx
ubuntu 安装brew
在UEFI启动模式下安装ubuntu

一、下载
igv下载地址：http://software.broadinstitute.org/software/igv/download
linux环境下的包的下载地址：https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_Linux_2.8.2.zip
二、解压和配置
unzip IGV_Linux_2.8.2.zip -d IGV
cd IGV/IGV_Linux_2.8.2
sh igv.sh

#报错信息
#echo Using bundled JDK.
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
openjdk version "11.0.5" 2019-10-15
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.5+10)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.5+10, mixed mode)
WARN [2020-05-23T15:49:42,495]  [Globals.java:139] [main]  Development mode is enabled
INFO [2020-05-23T15:49:42,523]  [DirectoryManager.java:179] [main]  IGV Directory: /home/whq/igv
INFO [2020-05-23T15:49:44,388]  [Main.java:159] [AWT-EventQueue-0]  Startup  IGV Version 2.8.2 03/23/2020 08:58 PM
INFO [2020-05-23T15:49:44,403]  [Main.java:160] [AWT-EventQueue-0]  Java 11.0.5 (build 11.0.5+10) 2019-10-15
INFO [2020-05-23T15:49:44,404]  [Main.java:163] [AWT-EventQueue-0]  Java Vendor: AdoptOpenJDK https://adoptopenjdk.net/
INFO [2020-05-23T15:49:44,405]  [Main.java:165] [AWT-EventQueue-0]  JVM: OpenJDK 64-Bit Server VM AdoptOpenJDK
INFO [2020-05-23T15:49:44,405]  [DirectoryManager.java:84] [AWT-EventQueue-0]  Fetching user directory...
INFO [2020-05-23T15:49:44,455]  [Main.java:168] [AWT-EventQueue-0]  Default User Directory: /home/whq
INFO [2020-05-23T15:49:44,456]  [Main.java:169] [AWT-EventQueue-0]  OS: Linux 5.3.0-42-generic amd64
ERROR [2020-05-23T15:49:44,461]  [DefaultExceptionHandler.java:49] [AWT-EventQueue-0]  Unhandled exception
java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.#该行为报错信息
        at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source) ~[?:?]
        at java.awt.Window.<init>(Unknown Source) ~[?:?]
        at java.awt.Frame.<init>(Unknown Source) ~[?:?]
        at java.awt.Frame.<init>(Unknown Source) ~[?:?]
        at javax.swing.JFrame.<init>(Unknown Source) ~[?:?]
        at org.broad.igv.ui.Main.lambda$main$0(Main.java:111) ~[igv.jar:?]
        at java.awt.event.InvocationEvent.dispatch(Unknown Source) ~[?:?]
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source) ~[?:?]
        at java.awt.EventQueue$4.run(Unknown Source) ~[?:?]
        at java.awt.EventQueue$4.run(Unknown Source) ~[?:?]
        at java.security.AccessController.doPrivileged(Native Method) ~[?:?]
        at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) ~[?:?]
        at java.awt.EventQueue.dispatchEvent(Unknown Source) ~[?:?]
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:?]
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:?]
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:?]
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?]
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:?]
        at java.awt.EventDispatchThread.run(Unknown Source) [?:?]
INFO [2020-05-23T15:49:45,795]  [ShutdownThread.java:46] [Thread-1]  Shutting down

一开始我以为是没有安装X11，参考链接为：https://blog.csdn.net/weixin_33804582/article/details/93528675
但是细查之下好像不是，应该是环境变量配置的问题，参考链接：https://www.cnblogs.com/EasonJim/p/6832657.html
所以需要修改环境变量
在~/.bashrc文件下加入代码行

export DISPLAY=:0.0

然后在重新加载一下bashrc

. ~/.bashrc

注意，我发现运行一次export DISPLAY=:0.0即可解决上述报错，但是如果把它加到bashrc中，可能会导致终端无法定位到能打开可视化界面的应用，即Xmanager和Xming可能无法被正常打开，导致无法可视化，因此还是只运行一次，不要把它加到环境变量中！！！在这边找原因找了一个下午，引以为戒！

然后再重新运行igv.sh即可,默认会占用60151端口，同时通过xmanager显示（我之前用的ubuntu子系统，应该是缺少展示可视化界面的应用（如xmanager或xming），所以无法自动弹出应用）

可以将igv.sh加入环境变量中
vim ~/.bashrc
方法一：进入文件后将下述语句添加到bashrc末尾
igv=/aboulute/path/to/igv.sh
保存退出，然后重新更新配置
. ~/.bashrc
之后每次启动igv时可以直接输入下面语句
sh $igv
方法二：在.bashrc中起个别名：alias igv='bash /aboulute/path/to/igv.sh' ##这样每次启动可以只使用命令 igv 来启动
参考链接：https://zhuanlan.zhihu.com/p/108571232

我理解的igv配置过程中的逻辑为：igv本身是可视化软件，需要依赖服务器上安装的可视化软件X11，同时由于用户是通过终端对服务器进行操作，因此需要操作终端的电脑上安装可以展示可视化图形的软件，一般为Xmanager或Xming，之后需要通过DISPLAY来指定在终端上输出的端口，这样就形成了 igv>X11>DISPLAY>Xmanager/Xming这样的可视化展示过程，最终让用户能看到igv的处理结果。为了之后的操作便利，需要在bashrc中预设变量，这样之后运行igv时就可以通过最短的代码运行，而不用大费周章地去找路径啦！

补充：在mac上如何远程连接远端服务器并进行可视化操作！：https://heartarea.github.io/2016/07/28/OSX%E4%BD%BF%E7%94%A8XQuartz%E8%BF%9C%E7%A8%8B%E8%BF%9E%E6%8E%A5Linux%E4%B8%BB%E6%9C%BA/

三、使用igv
参考链接：https://www.jianshu.com/p/e5338858dd82
参考链接：https://zhuanlan.zhihu.com/p/108571232
参考连接：https://blog.csdn.net/w7913766/article/details/80101414