【软件安装】---宏基因组分析软件qiime2的安装及使用

前言：QIIME 2是一款强大的、可扩展的、分散的微生物组分分析包，其重点是数据和分析透明度。QIIME 2能帮助研究人员分析原始测序数据，并得到出版物质量的数据和统计结果。

最新版本Qiime2

官方网址：https://docs.qiime2.org/2020.2/about/
安装qiime2
由于qiime2的配置文件需要使用conda安装很多依赖工具，所以首先需要下载qiime2-2020.2-py36-linux-conda.yml：
使用wget下载：

wget https://data.qiime2.org/distro/core/qiime2-2020.2-py36-linux-conda.yml

或者手动下载：

https://raw.githubusercontent.com/qiime2/environment-files/master/2020.2/release/qiime2-2020.2-py36-linux-conda.yml

使用conda安装qiime2：

#修改国内源
sed -i "s/conda-forge/https:\/\/mirrors.tuna.tsinghua.edu.cn\/anaconda\/cloud\/conda-forge/" qiime2-2020.2-py36-linux-conda.yml
sed -i "s/bioconda/https:\/\/mirrors.tuna.tsinghua.edu.cn\/anaconda\/cloud\/bioconda/" qiime2-2020.2-py36-linux-conda.yml
sed -i "/^- q2/d" qiime2-2020.2-py36-linux-conda.yml
sed -i "/^- qiime2/d" qiime2-2020.2-py36-linux-conda.yml

#安装qiime2
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml

激活qiime2虚拟环境：

source activate qiime2-2020.2

安装过程中如果有报错，如：

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/blast-2.9.0-pl526h3066fca_4.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/qiime2/label/r2020.2/linux-64/q2-deblur-2020.2.0-py36_0.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/qiime2/label/r2020.2/linux-64/q2-metadata-2020.2.0-py36_0.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

这时，需要把已安装的配置软件先删除，再重新安装一次，跟网络稳定性有关：

conda clean -y --all
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml

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最后编辑于：2020.06.10 17:02:00