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
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)