Trim Galore安装

安装这个Trim Galore软件上之前需要安装好Fastqc和cutadapt两个软件：

1. 安装Fastqc

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip

unzip fastqc_v0.11.8.zip

cd  /data/tools/FastQC

chmod u+x fastqc  或者 chmod 754 fastqc      #设置可执行权限

###配置环境变量

vim ~/.bashrc

export PATH="/data/tools/FastQC:$PATH"  # 添加至文件最后一行

source ~/.bashrc  #使配置文件生效

fastqc --help  #测试

2.安装cutadapt

cutadapt下载源代码：https://github.com/marcelm/cutadapt

1、conda 安装成功；但调用的时候一直出问题，也找不到原因，于是换成源码安装（捂脸。。）

2、尝试源码安装：

          git clone https://github.com/marcelm/cutadapt/

          cd cutadapt

          chmod 777 setup.py

          python setup.py 

然后就是遇到各种Python（报错）

configure: error: No modern nasm or yasm found as required. Nasm should be v2.11.01 or later (v2.13）

pkg_resources.VersionConflict: (PyYAML 3.11 (**********), Requirement.parse('pyyaml>=4'))

于是各种更新：

python3 -m pip install --upgrade pip -i https://pypi.douban.com/simple

python3 -m pip install nasm

python3 -m pip list

直到没有出现报错

cutadapt --version      #检查是否安装成功

###配置环境变量（同上）

3.安装Trim Galore

TrimGalore: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

3.1. 源代码下载：https://github.com/FelixKrueger/TrimGalore

查看安装日志：Installation：

Trim Galore!is a a Perl wrapper around two tools:CutadaptandFastQC. To use, ensure that these two pieces of software are available and copy the trim_galore script to a location available on the PATH.

For example:

#Check that cutadapt is installed

cutadapt --version

#Check that FastQC is installed

fastqc -v

#Install Trim Galore!

curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.4.5.tar.gz -o trim_galore.tar.gz 

tar xvzf trim_galore.tar.gz

TrimGalore-0.4.5/trim_galore            #检查是否安装成功

下载源码安装成功！

###配置环境变量（同上）