- trimmomatic:常用于处理原始测序数据
- GATK：功能强大，尤其是variant calling
- 下载
- 安装
- 运行：java-Xmx4G-jar xxx.jar parameters
Trimmomatic
# 下载安装解压
vip39@VM-0-15-ubuntu:~/opt/biosoft/Trimmomatic-0.38$ ls
adapters LICENSE trimmomatic-0.38.jar
# trimmomatic-0.38.jar该jar就是我们的执行目标,运行改命令使用以下程序：
vip39@VM-0-15-ubuntu:~/opt/biosoft/Trimmomatic-0.38$ java -Xmx16g -jar trimmomatic-0.38.jar
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
or:
-version
# 也可以绝对路径的方式运行
vip39@VM-0-15-ubuntu:~$ java -Xmx16g -jar ~/opt/biosoft/Trimmomatic-0.38/trimmomatic-0.38.jar
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
or:
-version
GATK
vip39@VM-0-15-ubuntu:~/opt/biosoft/gatk-4.0.11.0$ ls
gatk GATKConfig.EXAMPLE.properties gatkPythonPackageArchive.zip
gatk-completion.sh gatkdoc README.md
gatkcondaenv.intel.yml gatk-package-4.0.11.0-local.jar scripts
gatkcondaenv.yml gatk-package-4.0.11.0-spark.jar
vip39@VM-0-15-ubuntu:~/opt/biosoft/gatk-4.0.11.0$ java -Xmx16g -jar gatk-package-4.0.11.0-local.jar
# 将运行路径添加到环境变量，vim ~/.bashrc
export PATH=$PATH:~/opt/biosoft/ncbi-blast-2.7.1+/bin/:~/opt/sysoft/bin/tree
PATH=$PATH:~/opt/biosoft/wise2.4.1/src/bin/
export WISECONFIGDIR=~/opt/biosoft/wise2.4.1/wisecfg/
export PATH=~/opt/biosoft/gatk-4.0.11.0:$PATH
# 查看一下
vip39@VM-0-15-ubuntu:~$ vim ~/.bashrc
vip39@VM-0-15-ubuntu:~$ source ~/.bashrc
vip39@VM-0-15-ubuntu:~$ gatk #就可以运行gatk软件了
解决其它软件对Java的依赖
JAVA_HOME：java 所在目录
- 到Rstudio查看
> install.packages('rJava')
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rJava_0.9-10.zip'
Content type 'application/zip' length 826966 bytes (807 KB)
downloaded 807 KB
package ‘rJava’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Develop\AppData\Local\Temp\RtmpK8Ta30\downloaded_packages
> Sys.getenv("JAVA_HOME")
[1] ""
> library(rJava)
Error: package or namespace load failed for ‘rJava’:
loadNamespace()里算'rJava'时.onLoad失败了，详细内容：
调用: fun(libname, pkgname)
错误: JAVA_HOME cannot be determined from the Registry
- 安装java，查看java的运行路径
C:\Program Files\Java\jre1.8.0_191，添加到电脑的环境变量
JAVA_HOME
# 同样的再到Rstudio：
> Sys.getenv("JAVA_HOME")
[1] "C:\\Program Files\\Java\\jre1.8.0_191"
