安装qiime2实操记录
说在前头：部分图片由于过大，简书上传不了，笔者觉得简书的这篇博客应该够了。如果觉得目前简书版本看的不得劲，只能看公众号里的咯。
Qiime2的工作流程如下：
图片来源：https://www.jianshu.com/p/5a35eae1b707
图片来源：https://baijiahao.baidu.com/s?id=1693286972375193639&wfr=spider&for=pc
现在正式实操
该教程的精髓：qiime2也是存在镜像源的，它便是来自清华的镜像源，只要将他们的镜像源都进行更换，则可以轻松解决conda安装qiime2的问题。
1. 下载qiime2的conda的.yml文件——可以理解为一个要运行成功qiime2的依赖包清单
wget https://data.qiime2.org/distro/core/qiime2-2021.11-py38-linux-conda.yml
2. 修改下载好的.yml的镜像源，即channels这部分
原内容:
channels:
- qiime2/label/r2021.11
- conda-forge
- bioconda
- defaults
修改为：
channels:
-https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/qiime2
-https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
-https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
- defaults
也可以直接复制下面的文件内容->新建文本文件->粘贴保存->放在对应的位置，本教程是放在用户主目录下，即~或者/home/chenhuilong/
channels:
-https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/qiime2
-https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
-https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
-defaults
dependencies:
-_libgcc_mutex=0.1
-_openmp_mutex=4.5
-_r-mutex=1.0.1
-alsa-lib=1.2.3
-argcomplete=1.12.3
-argon2-cffi=21.1.0
-async_generator=1.10
-attrs=21.2.0
-backcall=0.2.0
-backports=1.0
-backports.functools_lru_cache=1.6.4
-bibtexparser=1.1.0
-binutils_impl_linux-64=2.36.1
-binutils_linux-64=2.36
-bioconductor-biobase=2.50.0
-bioconductor-biocgenerics=0.36.0
-bioconductor-biocparallel=1.24.1
-bioconductor-biostrings=2.58.0
-bioconductor-dada2=1.18.0
-bioconductor-delayedarray=0.16.3
-bioconductor-genomeinfodb=1.26.4
-bioconductor-genomeinfodbdata=1.2.4
-bioconductor-genomicalignments=1.26.0
-bioconductor-genomicranges=1.42.0
-bioconductor-iranges=2.24.1
-bioconductor-matrixgenerics=1.2.1
-bioconductor-rhtslib=1.22.0
-bioconductor-rsamtools=2.6.0
-bioconductor-s4vectors=0.28.1
-bioconductor-shortread=1.48.0
-bioconductor-summarizedexperiment=1.20.0
-bioconductor-xvector=0.30.0
-bioconductor-zlibbioc=1.36.0
-biom-format=2.1.10
-blast=2.12.0
-bleach=4.1.0
-bokeh=2.4.2
-bowtie2=2.4.2
-brotli=1.0.9
-brotli-bin=1.0.9
-brotlipy=0.7.0
-bwidget=1.9.14
-bzip2=1.0.8
-c-ares=1.18.1
-ca-certificates=2021.10.8
-cachecontrol=0.12.10
-cached-property=1.5.2
-cached_property=1.5.2
-cairo=1.16.0
-certifi=2021.10.8
-cffi=1.15.0
-chardet=4.0.0
-click=7.1.2
-colorama=0.4.4
-cryptography=35.0.0
-curl=7.80.0
-cutadapt=3.5
-cycler=0.11.0
-cython=0.29.24
-dbus=1.13.6
-deblur=1.1.0
-debugpy=1.5.1
-decorator=4.4.2
-defusedxml=0.7.1
-dendropy=4.5.2
-dill=0.3.4
-dnaio=0.6.0
-emperor=1.0.3
-entrez-direct=16.2
-entrypoints=0.3
-expat=2.4.1
-fastcluster=1.1.26
-fasttree=2.1.10
-font-ttf-dejavu-sans-mono=2.37
-font-ttf-inconsolata=3.000
-font-ttf-source-code-pro=2.038
-font-ttf-ubuntu=0.83
-fontconfig=2.13.1
-fonts-conda-ecosystem=1
-fonts-conda-forge=1
-fonttools=4.28.1
-freetype=2.10.4
-fribidi=1.0.10
-future=0.18.2
-gcc_impl_linux-64=9.4.0
-gcc_linux-64=9.4.0
-gettext=0.19.8.1
-gfortran_impl_linux-64=9.4.0
-gfortran_linux-64=9.4.0
-glib=2.70.1
-glib-tools=2.70.1
-gneiss=0.4.6
-graphite2=1.3.13
-gsl=2.7
-gst-plugins-base=1.18.5
-gstreamer=1.18.5
-gxx_impl_linux-64=9.4.0
-gxx_linux-64=9.4.0
-h5py=3.3.0
-harfbuzz=3.1.1
-hdf5=1.10.6
-hdmedians=0.14.2
-hmmer=3.1b2-htslib=1.14
-icu=68.2
-idna=2.10
-ijson=3.1.3
-importlib-metadata=4.8.2
-importlib_metadata=4.8.2
-importlib_resources=5.4.0
-iniconfig=1.1.1
-ipykernel=6.5.0
-ipython=7.29.0
-ipython_genutils=0.2.0
-ipywidgets=7.6.5
-iqtree=2.1.4_beta-isa-l=2.30.0
-jbig=2.1
-jedi=0.18.1
-jinja2=3.0.3
-joblib=1.1.0
-jpeg=9d-jq=1.6
-jsonschema=4.2.1
-jupyter_client=7.1.0
-jupyter_core=4.9.1
-jupyterlab_pygments=0.1.2
-jupyterlab_widgets=1.0.2
-kernel-headers_linux-64=2.6.32
-kiwisolver=1.3.2
-krb5=1.19.2
-lcms2=2.12
-ld_impl_linux-64=2.36.1
-lerc=2.2.1
-libblas=3.9.0
-libbrotlicommon=1.0.9
-libbrotlidec=1.0.9
-libbrotlienc=1.0.9
-libcblas=3.9.0
-libclang=11.1.0
-libcurl=7.80.0
-libdeflate=1.7
-libedit=3.1.20191231
-libev=4.33
-libevent=2.1.10
-libffi=3.4.2
-libgcc=7.2.0
-libgcc-devel_linux-64=9.4.0
-libgcc-ng=11.2.0
-libgfortran-ng=11.2.0
-libgfortran5=11.2.0
-libglib=2.70.1
-libgomp=11.2.0
-libiconv=1.16
-liblapack=3.9.0
-libllvm10=10.0.1
-libllvm11=11.1.0
-libnghttp2=1.43.0
-libnsl=2.0.0
-libogg=1.3.4
-libopenblas=0.3.18
-libopus=1.3.1
-libpng=1.6.37
-libpq=13.5
-libsanitizer=9.4.0
-libsodium=1.0.18
-libssh2=1.10.0
-libstdcxx-devel_linux-64=9.4.0
-libstdcxx-ng=11.2.0
-libtiff=4.3.0
-libuuid=2.32.1
-libuv=1.42.0
-libvorbis=1.3.7
-libwebp-base=1.2.1
-libxcb=1.13
-libxkbcommon=1.0.3
-libxml2=2.9.12
-libxslt=1.1.33
-libzlib=1.2.11
-llvmlite=0.36.0
-lockfile=0.12.2
-lxml=4.6.4
-lz4=3.1.3
-lz4-c=1.9.3
-mafft=7.490
-make=4.3
-markupsafe=2.0.1
-matplotlib=3.5.0
-matplotlib-base=3.5.0
-matplotlib-inline=0.1.3
-mistune=0.8.4
-more-itertools=8.11.0
-msgpack-python=1.0.2
-munkres=1.1.4
-mysql-common=8.0.27
-mysql-libs=8.0.27
-natsort=8.0.0
-nbclient=0.5.9
-nbconvert=6.3.0
-nbformat=5.1.3
-ncurses=6.2
-nest-asyncio=1.5.1
-networkx=2.6.3
-nodejs=16.12.0
-nose=1.3.7
-notebook=6.4.6
-nspr=4.32
-nss=3.72
-numba=0.53.1
-numpy=1.21.4
-olefile=0.46
-oniguruma=6.9.7.1
-openjdk=11.0.1
-openjpeg=2.4.0
-openssl=1.1.1l-packaging=21.3
-pandas=1.2.5
-pandoc=2.16.2
-pandocfilters=1.5.0
-pango=1.48.10
-parso=0.8.2
-patsy=0.5.2
-pbzip2=1.1.13
-pcre=8.45
-pcre2=10.37
-perl=5.26.2
-perl-archive-tar=2.18
-perl-carp=1.38
-perl-common-sense=3.74
-perl-compress-raw-bzip2=2.087
-perl-compress-raw-zlib=2.087
-perl-exporter=5.72
-perl-exporter-tiny=1.002001
-perl-extutils-makemaker=7.36
-perl-io-compress=2.087
-perl-io-zlib=1.10
-perl-json=4.02
-perl-json-xs=2.34
-perl-list-moreutils=0.413
-perl-pathtools=3.75
-perl-scalar-list-utils=1.52
-perl-threaded=5.26.0
-perl-types-serialiser=1.0
-pexpect=4.8.0
-pickleshare=0.7.5
-pigz=2.6
-pillow=8.4.0
-pip=21.3.1
-pixman=0.40.0
-pluggy=1.0.0
-prometheus_client=0.12.0
-prompt-toolkit=3.0.22
-psutil=5.8.0
-pthread-stubs=0.4
-ptyprocess=0.7.0
-py=1.11.0
-pycparser=2.21
-pygments=2.10.0
-pynndescent=0.5.5
-pyopenssl=21.0.0
-pyparsing=3.0.6
-pyqt=5.12.3
-pyqt-impl=5.12.3
-pyqt5-sip=4.19.18
-pyqtchart=5.12
-pyqtwebengine=5.12.1
-pyrsistent=0.18.0
-pysocks=1.7.1
-pytest=6.2.5
-python=3.8.12
-python-dateutil=2.8.2
-python-isal=0.11.1
-python_abi=3.8
-pytz=2021.3
-pyyaml=6.0
-pyzmq=22.3.0
-q2-alignment=2021.11.0
-q2-composition=2021.11.0
-q2-cutadapt=2021.11.0
-q2-dada2=2021.11.0
-q2-deblur=2021.11.0
-q2-demux=2021.11.0
-q2-diversity=2021.11.0
-q2-diversity-lib=2021.11.0
-q2-emperor=2021.11.0
-q2-feature-classifier=2021.11.0
-q2-feature-table=2021.11.0
-q2-fragment-insertion=2021.11.0
-q2-gneiss=2021.11.0
-q2-longitudinal=2021.11.0
-q2-metadata=2021.11.0
-q2-mystery-stew=2021.11.0
-q2-phylogeny=2021.11.0
-q2-quality-control=2021.11.0
-q2-quality-filter=2021.11.0
-q2-sample-classifier=2021.11.0
-q2-taxa=2021.11.0
-q2-types=2021.11.0
-q2-vsearch=2021.11.0
-q2cli=2021.11.0
-q2galaxy=2021.11.0
-q2templates=2021.11.0
-qiime2=2021.11.0
-qt=5.12.9
-r-assertthat=0.2.1
-r-backports=1.3.0
-r-base=4.0.5
-r-bh=1.75.0_0-r-bitops=1.0_7-r-brio=1.1.2
-r-callr=3.7.0
-r-cli=3.1.0
-r-cluster=2.1.2
-r-colorspace=2.0_2-r-crayon=1.4.2
-r-desc=1.4.0
-r-diffobj=0.3.5
-r-digest=0.6.28
-r-ellipsis=0.3.2
-r-evaluate=0.14
-r-fansi=0.5.0
-r-farver=2.1.0
-r-formatr=1.11
-r-futile.logger=1.4.3
-r-futile.options=1.0.1
-r-ggplot2=3.3.5
-r-glue=1.5.0
-r-gtable=0.3.0
-r-hwriter=1.3.2
-r-isoband=0.2.5
-r-jpeg=0.1_9-r-jsonlite=1.7.2
-r-labeling=0.4.2
-r-lambda.r=1.2.4
-r-lattice=0.20_45-r-latticeextra=0.6_29-r-lifecycle=1.0.1
-r-magrittr=2.0.1
-r-mass=7.3_54-r-matrix=1.3_2-r-matrixstats=0.61.0
-r-mgcv=1.8_38-r-munsell=0.5.0
-r-nlme=3.1_153-r-permute=0.9_5-r-pillar=1.6.4
-r-pkgconfig=2.0.3
-r-pkgload=1.2.3
-r-plyr=1.8.6
-r-png=0.1_7-r-praise=1.0.0
-r-processx=3.5.2
-r-ps=1.6.0
-r-r6=2.5.1
-r-rcolorbrewer=1.1_2-r-rcpp=1.0.7
-r-rcppparallel=5.1.4
-r-rcurl=1.98_1.5
-r-rematch2=2.1.2
-r-reshape2=1.4.4
-r-rlang=0.4.12
-r-rprojroot=2.0.2
-r-rstudioapi=0.13
-r-scales=1.1.1
-r-snow=0.4_4-r-stringi=1.7.5
-r-stringr=1.4.0
-r-testthat=3.1.0
-r-tibble=3.1.6
-r-utf8=1.2.2
-r-vctrs=0.3.8
-r-vegan=2.5_7-r-viridislite=0.4.0
-r-waldo=0.3.1
-r-withr=2.4.2
-raxml=8.2.12
-readline=8.1
-requests=2.25.1
-samtools=1.14
-scikit-bio=0.5.6
-scikit-learn=0.24.1
-scipy=1.7.2
-seaborn=0.11.2
-seaborn-base=0.11.2
-sed=4.8
-send2trash=1.8.0
-sepp=4.3.10
-setuptools=59.2.0
-six=1.16.0
-sortmerna=2.0
-sqlite=3.36.0
-statsmodels=0.13.1
-sysroot_linux-64=2.12
-tbb=2020.2
-terminado=0.12.1
-testpath=0.5.0
-threadpoolctl=3.0.0
-tk=8.6.11
-tktable=2.10
-toml=0.10.2
-tornado=6.1
-tqdm=4.62.3
-traitlets=5.1.1
-typing_extensions=4.0.0
-tzlocal=2.1
-umap-learn=0.5.2
-unicodedata2=13.0.0.post2-unifrac=0.20.2
-urllib3=1.26.7
-vsearch=2.7.0
-wcwidth=0.2.5
-webencodings=0.5.1
-wheel=0.37.0
-widgetsnbextension=3.5.2
-xmltodict=0.12.0
-xopen=1.2.1
-xorg-kbproto=1.0.7
-xorg-libice=1.0.10
-xorg-libsm=1.2.3
-xorg-libx11=1.7.2
-xorg-libxau=1.0.9
-xorg-libxdmcp=1.1.3
-xorg-libxext=1.3.4
-xorg-libxrender=0.9.10
-xorg-libxt=1.2.1
-xorg-renderproto=0.11.1
-xorg-xextproto=7.3.0
-xorg-xproto=7.0.31
-xz=5.2.5
-yaml=0.2.5
-yq=2.12.2
-zeromq=4.3.4
-zipp=3.6.0
-zlib=1.2.11
-zstd=1.5.0
3. 用conda下载安装qiime2
conda env create -n qiime2-2021.11 --file qiime2-2021.11-py38-linux-conda.yml
以上命令解释为根据qiime2-2021.11-py38-linux-conda.yml文件创建一个名为qiime2-2021.11的conda环境。-n也可以写作--name，自然--file也可以写作-f
# 这个命令跟网络有关，看运气，笔者尝试了4次，下载安装失败，然后弄别的，隔了很久，再次尝试，成功开始下载，但是由于这个依赖包太多太大，实测30+分钟安装时间。师姐的电脑和网络环境20+分钟，当然能够下载安装之前自然失败了很多次。——说这个，就是告诫读者，不要气馁，多尝试几次总能成功的。
4. 测试
按照conda给的提示，激活/打开这个conda环境
conda activate qiime2-2021.11
关闭自然是
conda deactivate
接下来就是好好去学习qiime2的使用了吧。。。
Reference
https://www.jianshu.com/p/0fcb83d8fb1f
