1. 官网

官网qiime2的conda方法安装教程官网：
https://docs.qiime2.org/2018.4/install/native/

由于docker的方法下载中断，无法安装。虚拟机的方法下载又太大，那就通过conda的方法来进行安装，解决软件的依赖关系。

2. 软件版本2018.04

• 下载
• 指定虚拟环境名称为qiime2-2018.4 ，指定软件的参数文件
• 安装成功后，删除软件参数配置文件

wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-linux-conda.yml
conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2018.4-py35-linux-conda.yml

3. 重用命令

# 删除虚拟环境
conda env remove -n qiime2-2018.4
# 删除下载失败的缓存包
conda clean -y --all

# 激活虚拟环境
source activate qiime2-2018.4
# 退出虚拟环境
source deactivate qiime2-2018.4

# 安装成功测试
qiime --help

4. 安装成功

$conda info --envs
# conda environments:
#
base                  *  /home/toucan/miniconda3
qiime1                   /home/toucan/miniconda3/envs/qiime1
qiime2-2018.4            /home/toucan/miniconda3/envs/qiime2-2018.4

5. 版本查看

$qiime info
System versions
Python version: 3.5.5
QIIME 2 release: 2018.4
QIIME 2 version: 2018.4.0
q2cli version: 2018.4.0

Installed plugins
alignment: 2018.4.0
composition: 2018.4.0
cutadapt: 2018.4.0
dada2: 2018.4.0
deblur: 2018.4.0
demux: 2018.4.0
diversity: 2018.4.0
emperor: 2018.4.0
feature-classifier: 2018.4.0
feature-table: 2018.4.0
gneiss: 2018.4.0
longitudinal: 2018.4.0
metadata: 2018.4.0
phylogeny: 2018.4.0
quality-control: 2018.4.0
quality-filter: 2018.4.0
sample-classifier: 2018.4.0
taxa: 2018.4.0
types: 2018.4.0
vsearch: 2018.4.0

Application config directory
/home/toucan/.config/q2cli

5. 帮助文档

$qiime --help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
/home/toucan/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/matplotlib/font_manager.py:278: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  'Matplotlib is building the font cache using fc-list. '
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.
  emperor             Plugin for ordination plotting with Emperor.
  feature-classifier  Plugin for taxonomic classification.
  feature-table       Plugin for working with sample by feature tables.
  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.