Qiime2(一)-安装

QIIME 2是一款功能强大、可扩展，去中心化的微生物组软件分析包，强调数据分析透明。QIIME 2可以使研究者从原始DNA序列开始分析，直接获取出版级的统计和图片结果。

1.安装

由于之前已经安装过Miniconda，此次不在安装。
https://www.jianshu.com/p/eb89ab4af035
官方安装文档:
https://qiime2.org/,依次点击Docs，Installing QIIME 2，Linux(64-bit)
点击Latest Docs，跳转到https://docs.qiime2.org/2019.4/install/native/
最新版本为qiime2-2020.11-py36-linux-conda.yml

1.1下载文件

wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-linux-conda.yml
##下载失败，换用：
wget -c http://210.75.224.110/github/QIIME2ChineseManual/2020.11/qiime2-2020.11-py36-linux-conda.yml
time conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml

1.2 conda创建环境 -n 环境名称

time conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml
#real   26m3.672s
#user   3m15.193s
#sys    0m11.148s

1.3 可选步骤，删除刚才下载的文件

rm qiime2-2020.6-py36-linux-conda.yml

1.4 激活或停用conda环境，运行

conda info --envs
# To activate this environment, use
#     $ conda activate qiime2-2020.11
# To deactivate an active environment, use
#     $ conda deactivate

1.5 测试

qiime --help

如果运行此命令时未报告任何错误，则安装成功！

Usage: qiime [OPTIONS] COMMAND [ARGS]...

  QIIME 2 command-line interface (q2cli)
  --------------------------------------

  To get help with QIIME 2, visit https://qiime2.org.

  To enable tab completion in Bash, run the following command or add it to
  your .bashrc/.bash_profile:

      source tab-qiime

  To enable tab completion in ZSH, run the following commands or add them to
  your .zshrc:

      autoload bashcompinit && bashcompinit && source tab-qiime

Options:
  --version   Show the version and exit.
  --help      Show this message and exit.

Commands:
  info                Display information about current deployment.
  tools               Tools for working with QIIME 2 files.
  dev                 Utilities for developers and advanced users.
  alignment           Plugin for generating and manipulating alignments.
  composition         Plugin for compositional data analysis.
  cutadapt            Plugin for removing adapter sequences, primers, and
                      other unwanted sequence from sequence data.

  dada2               Plugin for sequence quality control with DADA2.
  deblur              Plugin for sequence quality control with Deblur.
  demux               Plugin for demultiplexing & viewing sequence quality.
  diversity           Plugin for exploring community diversity.
  diversity-lib       Plugin for computing community diversity.
  emperor             Plugin for ordination plotting with Emperor.
  feature-classifier  Plugin for taxonomic classification.
  feature-table       Plugin for working with sample by feature tables.
  fragment-insertion  Plugin for extending phylogenies.
  gneiss              Plugin for building compositional models.
  longitudinal        Plugin for paired sample and time series analyses.
  metadata            Plugin for working with Metadata.
  phylogeny           Plugin for generating and manipulating phylogenies.
  quality-control     Plugin for quality control of feature and sequence data.
  quality-filter      Plugin for PHRED-based filtering and trimming.
  sample-classifier   Plugin for machine learning prediction of sample
                      metadata.

  taxa                Plugin for working with feature taxonomy annotations.
  vsearch             Plugin for clustering and dereplicating with vsearch.

1.7删除旧版本的QIIME 2

conda env remove -n qiime2-2020.11

可以瞬间删除你这么久安装的环境。