生信分析中最主要的莫过于安装分析软件配置环境，conda的出现大大降低了软件的安装难度；当然conda也存在很多问题:篡改你的python版本,网速慢等问题,而清华的镜像站点也及其不稳定，所以想尽一切方法改善你的网速才是最终方案。推荐安装Ubuntu20.04来搭建分析环境，用了之后你会真的爱上他，安装请参考：https://www.jianshu.com/p/b24f3a06a905
conda install
conda官网下载不同系统的
https://docs.conda.io/en/latest/miniconda.html conda
wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
一路回车，yes不要做任何更改
vim .condarc 添加conda镜像站点
channels:
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- bioconda
- defaults
- r
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
- conda-forge
show_channel_urls: true
至此已经完成了conda安装及配置，下面安装qiime2用于微生物多样性-扩增子分析
1. qiime2安装方法(一）
wget https://data.qiime2.org/distro/core/qiime2-2020.8-py36-linux-conda.yml
创建qiime2环境根据官方文件用于安装(注：如果下载官方文件失败，请改善自己的网络环境)
文件链接: https://pan.baidu.com/s/1yjU5B9kQ_vIYmidfLa72Tg 密码: 1jdn
为了方便我将qiime2-2020.8-py36-linux-conda.yml内容复制到了文章末尾，只需要将其内容粘贴进文本中更改文件名称即可
下载实在是太难了！！！！
大家可以将文件中的安装源替换成清华镜像源，具体参考：
https://www.jianshu.com/p/fc890d01efbb
由于没有做测试我不在此进行修改
conda env create -n qiime2-2020.8 --file qiime2-2020.8-py36-linux-conda.yml
安装时间视个人网络环境，测试时不到20分钟安装完成
2. qiime2安装方法(二）
conda install -c qiime2/label/r2020.8 qiime2
conda官网已经给出直接安装的命令，更加的方便简洁
3. qiime2使用
查看已经创建的环境
conda env list
激活环境
conda activate qiime2-2020.8
关闭环境
conda deactivate
ubuntu 20.04.png
channels:
- qiime2/label/r2020.8
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- alsa-lib=1.2.3
- arb-bio-tools=6.0.6
- argon2-cffi=20.1.0
- attrs=20.1.0
- backcall=0.2.0
- backports=1.0
- backports.functools_lru_cache=1.6.1
- bibtexparser=1.1.0
- binutils_impl_linux-64=2.34
- binutils_linux-64=2.34
- bioconductor-biobase=2.42.0
- bioconductor-biocgenerics=0.28.0
- bioconductor-biocparallel=1.16.6
- bioconductor-biostrings=2.50.2
- bioconductor-dada2=1.10.0
- bioconductor-delayedarray=0.8.0
- bioconductor-genomeinfodb=1.18.1
- bioconductor-genomeinfodbdata=1.2.1
- bioconductor-genomicalignments=1.18.1
- bioconductor-genomicranges=1.34.0
- bioconductor-iranges=2.16.0
- bioconductor-rsamtools=1.34.0
- bioconductor-s4vectors=0.20.1
- bioconductor-shortread=1.40.0
- bioconductor-summarizedexperiment=1.12.0
- bioconductor-xvector=0.22.0
- bioconductor-zlibbioc=1.28.0
- biom-format=2.1.8
- blas=2.17
- blast=2.9.0
- bleach=3.1.5
- bokeh=2.1.1
- boost-cpp=1.70.0
- bowtie2=2.4.1
- brotlipy=0.7.0
- bwidget=1.9.14
- bzip2=1.0.8
- ca-certificates=2020.6.20
- cachecontrol=0.12.6
- cairo=1.16.0
- certifi=2020.6.20
- cffi=1.14.1
- chardet=3.0.4
- click=7.1.2
- cryptography=3.0
- curl=7.68.0
- cutadapt=2.10
- cycler=0.10.0
- cython=0.29.21
- deblur=1.1.0
- decorator=4.4.2
- defusedxml=0.6.0
- dendropy=4.4.0
- dnaio=0.4.2
- emperor=1.0.1
- entrez-direct=13.3
- entrypoints=0.3
- expat=2.2.9
- fastcluster=1.1.26
- fasttree=2.1.10
- fontconfig=2.13.1
- freetype=2.10.2
- fribidi=1.0.10
- future=0.18.2
- gcc_impl_linux-64=7.5.0
- gcc_linux-64=7.5.0
- gettext=0.19.8.1
- gfortran_impl_linux-64=7.5.0
- gfortran_linux-64=7.5.0
- giflib=5.2.1
- glib=2.65.0
- gneiss=0.4.6
- graphite2=1.3.13
- gsl=2.5
- gxx_impl_linux-64=7.5.0
- gxx_linux-64=7.5.0
- h5py=2.10.0
- harfbuzz=2.4.0
- hdf5=1.10.6
- hdmedians=0.13
- hmmer=3.1b2
- htslib=1.10.2
- icu=64.2
- idna=2.10
- ijson=3.1.1
- importlib-metadata=1.7.0
- importlib_metadata=1.7.0
- iniconfig=1.0.1
- ipykernel=5.3.4
- ipython=7.16.1
- ipython_genutils=0.2.0
- ipywidgets=7.5.1
- iqtree=2.0.3
- jedi=0.17.2
- jinja2=2.11.2
- joblib=0.16.0
- jpeg=9d
- jsonschema=3.2.0
- jupyter_client=6.1.6
- jupyter_core=4.6.3
- kiwisolver=1.2.0
- krb5=1.16.4
- lcms2=2.11
- ld_impl_linux-64=2.34
- libarbdb=6.0.6
- libblas=3.8.0
- libcblas=3.8.0
- libcurl=7.68.0
- libdeflate=1.3
- libedit=3.1.20191231
- libffi=3.2.1
- libgcc=7.2.0
- libgcc-ng=9.3.0
- libgfortran-ng=7.5.0
- libgomp=9.3.0
- libiconv=1.16
- liblapack=3.8.0
- liblapacke=3.8.0
- libopenblas=0.3.10
- libpng=1.6.37
- libsodium=1.0.18
- libssh2=1.9.0
- libstdcxx-ng=9.3.0
- libtiff=4.1.0
- libuuid=2.32.1
- libwebp-base=1.1.0
- libxcb=1.13
- libxml2=2.9.10
- llvm-openmp=10.0.1
- lockfile=0.12.2
- lz4-c=1.9.2
- mafft=7.471
- make=4.3
- markupsafe=1.1.1
- matplotlib=3.2.2
- matplotlib-base=3.2.2
- mistune=0.8.4
- more-itertools=8.4.0
- msgpack-python=1.0.0
- natsort=7.0.1
- nbconvert=5.6.1
- nbformat=5.0.7
- ncurses=6.1
- networkx=2.4
- nose=1.3.7
- notebook=6.1.3
- numpy=1.19.1
- olefile=0.46
- openjdk=11.0.8
- openssl=1.1.1g
- packaging=20.4
- pandas=0.25.3
- pandoc=2.10.1
- pandocfilters=1.4.2
- pango=1.42.4
- parso=0.7.1
- patsy=0.5.1
- pcre=8.44
- perl=5.26.2
- perl-app-cpanminus=1.7044
- perl-archive-tar=2.32
- perl-base=2.23
- perl-business-isbn=3.004
- perl-business-isbn-data=20140910.003
- perl-carp=1.38
- perl-common-sense=3.74
- perl-compress-raw-bzip2=2.087
- perl-compress-raw-zlib=2.087
- perl-constant=1.33
- perl-data-dumper=2.173
- perl-digest-hmac=1.03
- perl-digest-md5=2.55
- perl-encode=2.88
- perl-encode-locale=1.05
- perl-exporter=5.72
- perl-exporter-tiny=1.002001
- perl-extutils-makemaker=7.36
- perl-file-listing=6.04
- perl-file-path=2.16
- perl-file-temp=0.2304
- perl-html-parser=3.72
- perl-html-tagset=3.20
- perl-html-tree=5.07
- perl-http-cookies=6.04
- perl-http-daemon=6.01
- perl-http-date=6.02
- perl-http-message=6.18
- perl-http-negotiate=6.01
- perl-io-compress=2.087
- perl-io-html=1.001
- perl-io-socket-ssl=2.066
- perl-io-zlib=1.10
- perl-json=4.02
- perl-json-xs=2.34
- perl-libwww-perl=6.39
- perl-list-moreutils=0.428
- perl-list-moreutils-xs=0.428
- perl-lwp-mediatypes=6.04
- perl-lwp-protocol-https=6.07
- perl-mime-base64=3.15
- perl-mozilla-ca=20180117
- perl-net-http=6.19
- perl-net-ssleay=1.88
- perl-ntlm=1.09
- perl-parent=0.236
- perl-pathtools=3.75
- perl-scalar-list-utils=1.52
- perl-socket=2.027
- perl-storable=3.15
- perl-test-requiresinternet=0.05
- perl-time-local=1.28
- perl-try-tiny=0.30
- perl-types-serialiser=1.0
- perl-uri=1.76
- perl-www-robotrules=6.02
- perl-xml-namespacesupport=1.12
- perl-xml-parser=2.44_01
- perl-xml-sax=1.02
- perl-xml-sax-base=1.09
- perl-xml-sax-expat=0.51
- perl-xml-simple=2.25
- perl-xsloader=0.24
- pexpect=4.8.0
- pickleshare=0.7.5
- pigz=2.3.4
- pillow=7.2.0
- pip=20.2.2
- pixman=0.38.0
- pluggy=0.13.1
- prometheus_client=0.8.0
- prompt-toolkit=3.0.6
- psutil=5.7.2
- pthread-stubs=0.4
- ptyprocess=0.6.0
- py=1.9.0
- pycparser=2.20
- pygments=2.6.1
- pyopenssl=19.1.0
- pyparsing=2.4.7
- pyrsistent=0.16.0
- pysocks=1.7.1
- pytest=6.0.1
- python=3.6.10
- python-dateutil=2.8.1
- python_abi=3.6
- pytz=2020.1
- pyyaml=5.3.1
- pyzmq=19.0.2
- q2-alignment=2020.8.0
- q2-composition=2020.8.0
- q2-cutadapt=2020.8.0
- q2-dada2=2020.8.0
- q2-deblur=2020.8.0
- q2-demux=2020.8.0
- q2-diversity=2020.8.0
- q2-diversity-lib=2020.8.0
- q2-emperor=2020.8.0
- q2-feature-classifier=2020.8.0
- q2-feature-table=2020.8.0
- q2-fragment-insertion=2020.8.0
- q2-gneiss=2020.8.0
- q2-longitudinal=2020.8.0
- q2-metadata=2020.8.0
- q2-phylogeny=2020.8.0
- q2-quality-control=2020.8.0
- q2-quality-filter=2020.8.0
- q2-sample-classifier=2020.8.0
- q2-taxa=2020.8.0
- q2-types=2020.8.0
- q2-vsearch=2020.8.0
- q2cli=2020.8.0
- q2templates=2020.8.0
- qiime2=2020.8.0
- r-assertthat=0.2.1
- r-backports=1.1.6
- r-base=3.5.1
- r-bh=1.72.0_3
- r-bitops=1.0_6
- r-callr=3.4.3
- r-cli=2.0.2
- r-cluster=2.1.0
- r-colorspace=1.4_1
- r-crayon=1.3.4
- r-data.table=1.12.8
- r-desc=1.2.0
- r-digest=0.6.25
- r-ellipsis=0.3.0
- r-evaluate=0.14
- r-fansi=0.4.1
- r-farver=2.0.3
- r-formatr=1.7
- r-futile.logger=1.4.3
- r-futile.options=1.0.1
- r-ggplot2=3.3.0
- r-glue=1.4.0
- r-gtable=0.3.0
- r-hwriter=1.3.2
- r-isoband=0.2.1
- r-labeling=0.3
- r-lambda.r=1.2.4
- r-lattice=0.20_41
- r-latticeextra=0.6_28
- r-lifecycle=0.2.0
- r-magrittr=1.5
- r-mass=7.3_51.6
- r-matrix=1.2_18
- r-matrixstats=0.56.0
- r-mgcv=1.8_31
- r-munsell=0.5.0
- r-nlme=3.1_147
- r-permute=0.9_5
- r-pillar=1.4.3
- r-pkgbuild=1.0.7
- r-pkgconfig=2.0.3
- r-pkgload=1.0.2
- r-plyr=1.8.6
- r-praise=1.0.0
- r-prettyunits=1.1.1
- r-processx=3.4.2
- r-ps=1.3.2
- r-r6=2.4.1
- r-rcolorbrewer=1.1_2
- r-rcpp=1.0.4.6
- r-rcppparallel=5.0.0
- r-rcurl=1.98_1.2
- r-reshape2=1.4.4
- r-rlang=0.4.5
- r-rprojroot=1.3_2
- r-rstudioapi=0.11
- r-scales=1.1.0
- r-snow=0.4_3
- r-stringi=1.4.6
- r-stringr=1.4.0
- r-testthat=2.3.2
- r-tibble=3.0.1
- r-utf8=1.1.4
- r-vctrs=0.2.4
- r-vegan=2.5_6
- r-viridislite=0.3.0
- r-withr=2.2.0
- r-zeallot=0.1.0
- raxml=8.2.12
- readline=8.0
- requests=2.24.0
- samtools=1.10
- scikit-bio=0.5.5
- scikit-learn=0.23.1
- scipy=1.5.2
- seaborn=0.10.1
- seaborn-base=0.10.1
- send2trash=1.5.0
- sepp=4.3.10
- setuptools=49.6.0
- sina=1.7.1
- six=1.15.0
- sortmerna=2.0
- sqlite=3.32.3
- statsmodels=0.11.1
- tbb=2020.1
- terminado=0.8.3
- testpath=0.4.4
- threadpoolctl=2.1.0
- tk=8.6.10
- tktable=2.10
- toml=0.10.1
- tornado=6.0.4
- traitlets=4.3.3
- typing_extensions=3.7.4.2
- tzlocal=2.1
- unifrac=0.10.0
- urllib3=1.25.10
- vsearch=2.7.0
- wcwidth=0.2.5
- webencodings=0.5.1
- wheel=0.35.1
- widgetsnbextension=3.5.1
- xopen=0.9.0
- xorg-fixesproto=5.0
- xorg-inputproto=2.3.2
- xorg-kbproto=1.0.7
- xorg-libice=1.0.10
- xorg-libsm=1.2.3
- xorg-libx11=1.6.11
- xorg-libxau=1.0.9
- xorg-libxdmcp=1.1.3
- xorg-libxext=1.3.4
- xorg-libxfixes=5.0.3
- xorg-libxi=1.7.10
- xorg-libxrender=0.9.10
- xorg-libxtst=1.2.3
- xorg-recordproto=1.14.2
- xorg-renderproto=0.11.1
- xorg-xextproto=7.3.0
- xorg-xproto=7.0.31
- xz=5.2.5
- yaml=0.2.5
- zeromq=4.3.2
- zipp=3.1.0
- zlib=1.2.11
- zstd=1.4.5