从yaml创建conda环境(冲突)

Question

我遇到了一个问题，我的conda环境不是从.yaml文件创建的。我认为它失败是因为这个yaml文件是在centos6上制作的，但我后来在亚马逊上升级到了一个新的centos7 AMI。

conda env create --name html_ribo_report --file=html_ribo_report.yaml

没有错误，似乎在发现冲突后完成(运行大约一个小时)。如果需要，我可以粘贴输出。

以下是html_ribo_report.yaml的内容：

name: eclipsebio
channels:
  - https://repo.continuum.io/pkgs/free
  - defaults
  - conda-forge
  - bioconda
dependencies:
  - _libgcc_mutex=0.1=main
  - _r-mutex=1.0.0=anacondar_1
  - aioeasywebdav=2.2.0=py36_0
  - aiohttp=2.2.5=py36h3a1b670_0
  - altair=3.0.1=py36_0
  - appdirs=1.4.3=py36_0
  - argcomplete=1.8.2=py36_0
  - argh=0.26.2=py36_1
  - asn1crypto=0.22.0=py36h265ca7c_1
  - async-timeout=2.0.0=py36h92a791d_0
  - backports=1.0=py36hfa02d7e_1
  - backports.functools_lru_cache=1.4=py36_1
  - bamtools=2.4.0=3
  - bcftools=1.6=0
  - bedtools=2.26.0=0
  - bioawk=1.0=1
  - bioconductor-annotate=1.56.0=r3.4.1_0
  - bioconductor-annotationdbi=1.40.0=r3.4.1_0
  - bioconductor-biobase=2.38.0=r3.4.1_0
  - bioconductor-biocgenerics=0.24.0=r3.4.1_0
  - bioconductor-biocinstaller=1.28.0=r3.4.1_0
  - bioconductor-biocparallel=1.12.0=r3.4.1_0
  - bioconductor-biocstyle=2.6.0=r3.4.1_0
  - bioconductor-biomart=2.34.0=r3.4.1_0
  - bioconductor-biostrings=2.46.0=r3.4.1_0
  - bioconductor-bsgenome=1.46.0=r3.4.1_0
  - bioconductor-bumphunter=1.20.0=r3.4.1_0
  - bioconductor-delayedarray=0.4.1=r3.4.1_0
  - bioconductor-derfinder=1.12.0=r3.4.1_0
  - bioconductor-derfinderhelper=1.12.0=r3.4.1_0
  - bioconductor-edger=3.20.1=r3.4.1_0
  - bioconductor-genefilter=1.60.0=r3.4.1_0
  - bioconductor-geneplotter=1.56.0=r3.4.1_0
  - bioconductor-genomeinfodb=1.14.0=r3.4.1_0
  - bioconductor-genomeinfodbdata=1.1.0=r341_0
  - bioconductor-genomicalignments=1.14.0=r3.4.1_0
  - bioconductor-genomicfeatures=1.26.4=r3.4.1_0
  - bioconductor-genomicfiles=1.14.0=r3.4.1_0
  - bioconductor-genomicranges=1.30.0=r3.4.1_0
  - bioconductor-glimma=1.6.0=r3.4.1_0
  - bioconductor-iranges=2.12.0=r3.4.1_0
  - bioconductor-limma=3.34.1=r3.4.1_0
  - bioconductor-qvalue=2.10.0=r3.4.1_0
  - bioconductor-rsamtools=1.30.0=r3.4.1_0
  - bioconductor-rtracklayer=1.38.0=r3.4.1_0
  - bioconductor-s4vectors=0.16.0=r3.4.1_0
  - bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
  - bioconductor-tximport=1.6.0=r3.4.1_0
  - bioconductor-variantannotation=1.20.3=r3.4.1_0
  - bioconductor-xvector=0.18.0=r3.4.1_0
  - bioconductor-zlibbioc=1.24.0=r3.4.1_0
  - biopython=1.69=np113py36_0
  - blas=1.0=mkl
  - bleach=2.1.1=py36hd521086_0
  - boto=2.48.0=py36h6e4cd66_1
  - boto3=1.4.7=py36h4cc92d5_0
  - botocore=1.7.20=py36h085fff1_0
  - bowtie=1.2.3=py36hc9558a2_0
  - bowtie2=2.3.5=py36he860b03_0
  - bzip2=1.0.6=h0376d23_1
  - ca-certificates=2017.08.26=h1d4fec5_0
  - cairo=1.14.8=0
  - certifi=2016.9.26=py36_0
  - cffi=1.10.0=py36had8d393_1
  - chardet=3.0.4=py36h0f667ec_1
  - click=6.7=py36h5253387_0
  - configargparse=0.12.0=py36_0
  - cookies=2.2.1=py36_0
  - cryptography=2.0.3=py36ha225213_1
  - curl=7.52.1=0
  - cutadapt=2.7=py36h516909a_0
  - cycler=0.10.0=py36h93f1223_0
  - cython=0.28.5=py36hf484d3e_0
  - dbus=1.10.20=0
  - decorator=4.1.2=py36hd076ac8_0
  - dicttoxml=1.7.4=py36_0
  - dnaio=0.4.1=py36h516909a_0
  - docopt=0.6.2=py36_0
  - docutils=0.14=py36hb0f60f5_0
  - dropbox=7.3.1=py36_0
  - entrypoints=0.2.3=py36h1aec115_2
  - expat=2.2.4=h6ea4f2b_2
  - fastqc=0.11.6=2
  - filechunkio=1.8=py36_1
  - flask=0.12.2=py36hb24657c_0
  - font-ttf-dejavu-sans-mono=2.37=h6964260_0
  - font-ttf-inconsolata=2.001=hcb22688_0
  - font-ttf-source-code-pro=2.030=h7457263_0
  - fontconfig=2.12.1=3
  - freetype=2.5.5=2
  - ftputil=3.3.1=py36_0
  - future=0.16.0=py36_1
  - gettext=0.19.8.1=hd7bead4_3
  - gffutils=0.9=py36_0
  - glib=2.50.2=1
  - gmp=6.1.2=h6c8ec71_1
  - graphite2=1.3.10=hc526e54_0
  - gsl=2.2.1=h0c605f7_3
  - gst-plugins-base=1.8.0=0
  - gstreamer=1.8.0=0
  - harfbuzz=0.9.39=2
  - homer=4.10=pl526hc9558a2_0
  - html5lib=0.999999999=py36h2cfc398_0
  - htseq=0.9.1=py36_0
  - htslib=1.6=0
  - icu=54.1=0
  - idna=2.6=py36h82fb2a8_1
  - intel-openmp=2018.0.0=h15fc484_7
  - ipykernel=4.6.1=py36hbf841aa_0
  - ipython=6.2.1=py36h88c514a_1
  - ipython_genutils=0.2.0=py36hb52b0d5_0
  - itsdangerous=0.24=py36h93cc618_1
  - jbig=2.1=hdba287a_0
  - jedi=0.11.0=py36hf290c5b_0
  - jinja2=2.9.6=py36h489bce4_1
  - jmespath=0.9.3=py36hd3948f9_0
  - jpeg=9b=h024ee3a_2
  - jsonschema=2.6.0=py36h006f8b5_0
  - jupyter_client=5.1.0=py36h614e9ea_0
  - jupyter_core=4.4.0=py36h7c827e3_0
  - krb5=1.14.2=hcdc1b81_6
  - libedit=3.1.20170329=0
  - libffi=3.2.1=hd88cf55_4
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=8.2.0=hdf63c60_1
  - libgfortran-ng=7.2.0=h9f7466a_2
  - libiconv=1.14=0
  - libpng=1.6.36=hbc83047_0
  - libsodium=1.0.15=hf101ebd_0
  - libssh2=1.8.0=h2d05a93_3
  - libstdcxx-ng=9.1.0=hdf63c60_0
  - libtiff=4.0.9=h28f6b97_0
  - libuuid=2.32.1=h14c3975_1000
  - libxcb=1.12=h84ff03f_3
  - libxml2=2.9.4=0
  - markupsafe=1.0=py36hd9260cd_1
  - matplotlib=2.0.2=np113py36_0
  - matplotlib-venn=0.11.5=py_1
  - mistune=0.8.1=py36h3d5977c_0
  - mkl=2018.0.0=hb491cac_4
  - mock=2.0.0=py36h3c5bf6c_0
  - moto=1.1.1=py36_0
  - multidict=3.2.0=py36h97a4c74_0
  - mysql=5.5.24=0
  - mysql-connector-c=6.1.6=0
  - nbconvert=5.3.1=py36hb41ffb7_0
  - nbformat=4.4.0=py36h31c9010_0
  - ncurses=5.9=10
  - notebook=5.2.2=py36h40a37e6_0
  - numpy=1.13.3=py36ha12f23b_0
  - openjdk=8.0.121=1
  - openssl=1.0.2r=h7b6447c_0
  - pandas=0.21.0=py36h78bd809_1
  - pandoc=1.19.2.1=hea2e7c5_1
  - pandocfilters=1.4.2=py36ha6701b7_1
  - pango=1.40.3=1
  - paramiko=2.1.2=py36_0
  - parso=0.1.0=py36h2b61f4d_0
  - patsy=0.4.1=py36ha3be15e_0
  - pbr=3.1.1=py36hb5f6b33_0
  - pcre=8.39=1
  - perl=5.26.2=h14c3975_0
  - perl-common-sense=3.74=pl526_2
  - perl-json=4.02=pl526_0
  - perl-json-xs=2.34=pl526h6bb024c_3
  - perl-types-serialiser=1.0=pl526_2
  - pexpect=4.3.0=py36h673ed17_0
  - pickleshare=0.7.4=py36h63277f8_0
  - pigz=2.3=0
  - pip=9.0.1=py36h6c6f9ce_4
  - pixman=0.34.0=hceecf20_3
  - prompt_toolkit=1.0.15=py36h17d85b1_0
  - psutil=5.4.0=py36h84c53db_0
  - ptyprocess=0.5.2=py36h69acd42_0
  - pyaml=17.10.0=py_0
  - pyasn1=0.3.7=py36h0f28794_0
  - pybedtools=0.7.10=py36_1
  - pycparser=2.18=py36hf9f622e_1
  - pyfaidx=0.5.0=py36_0
  - pygments=2.2.0=py36h0d3125c_0
  - pyopenssl=17.2.0=py36h5cc804b_0
  - pyparsing=2.2.0=py36hee85983_1
  - pyqt=5.6.0=py36_2
  - pysam=0.11.2.2=py36_1
  - pysftp=0.2.9=py36_0
  - pysocks=1.6.7=py36hd97a5b1_1
  - python=3.6.3=h1284df2_4
  - python-dateutil=2.6.1=py36h88d3b88_1
  - pytz=2017.2=py36hc2ccc2a_1
  - pyyaml=3.12=py36hafb9ca4_1
  - pyzmq=16.0.3=py36he2533c7_0
  - qt=5.6.2=5
  - qualimap=2.2.2a=1
  - r-acepack=1.4.1=r3.4.1_0
  - r-assertthat=0.2.0=r3.4.1_0
  - r-backports=1.1.0=r3.4.1_0
  - r-base=3.4.1=0
  - r-base64enc=0.1_3=r3.4.1_0
  - r-bh=1.62.0_1=r3.4.1_0
  - r-bitops=1.0_6=r3.4.1_2
  - r-bookdown=0.4=r3.4.1_0
  - r-catools=1.17.1=r3.4.1_2
  - r-checkmate=1.8.2=r3.4.1_0
  - r-cluster=2.0.6=r3.4.1_0
  - r-codetools=0.2_15=r3.4.1_0
  - r-colorspace=1.3_2=r3.4.1_0
  - r-data.table=1.10.4=r3.4.1_0
  - r-dbi=0.6_1=r3.4.1_0
  - r-dichromat=2.0_0=r3.4.1_2
  - r-digest=0.6.12=r3.4.1_0
  - r-dorng=1.6.6=r3.4.1_0
  - r-evaluate=0.10=r3.4.1_0
  - r-foreach=1.4.3=r3.4.1_0
  - r-foreign=0.8_68=r3.4.1_0
  - r-formula=1.2_1=r3.4.1_0
  - r-futile.logger=1.4.3=r3.4.1_0
  - r-futile.options=1.0.0=r3.4.1_0
  - r-gdata=2.18.0=r3.4.1_0
  - r-getopt=1.20.0=r3.4.1_0
  - r-ggplot2=2.2.1=r3.4.1_0
  - r-gplots=3.0.1=r3.4.1_0
  - r-gridextra=2.2.1=r3.4.1_0
  - r-gtable=0.2.0=r3.4.1_0
  - r-gtools=3.5.0=r3.4.1_0
  - r-highr=0.6=r3.4.1_0
  - r-hmisc=4.0_3=r3.4.1_0
  - r-htmltable=1.9=r3.4.1_0
  - r-htmltools=0.3.6=r3.4.1_0
  - r-htmlwidgets=0.8=r3.4.1_1
  - r-iterators=1.0.8=r3.4.1_0
  - r-jsonlite=1.5=r3.4.1_0
  - r-kernsmooth=2.23_15=r3.4.1_0
  - r-knitr=1.16=r3.4.1_0
  - r-knitrbootstrap=1.0.1=r3.4.1_0
  - r-labeling=0.3=r3.4.1_2
  - r-lambda.r=1.1.9=r3.4.1_0
  - r-lattice=0.20_35=r3.4.1_0
  - r-latticeextra=0.6_28=r3.4.1_0
  - r-lazyeval=0.2.0=r3.4.1_0
  - r-locfit=1.5_9.1=r3.4.1_0
  - r-magrittr=1.5=r3.4.1_2
  - r-markdown=0.8=r3.4.1_0
  - r-mass=7.3_47=r3.4.1_0
  - r-matrix=1.2_10=r3.4.1_0
  - r-matrixstats=0.52.2=r3.4.1_0
  - r-memoise=1.1.0=r3.4.1_0
  - r-mime=0.5=r3.4.1_0
  - r-munsell=0.4.3=r3.4.1_0
  - r-nnet=7.3_12=r3.4.1_0
  - r-pkgmaker=0.22=r3.4.1_0
  - r-plogr=0.1_1=r3.4.1_0
  - r-plyr=1.8.4=r3.4.1_0
  - r-prettyunits=1.0.2=r3.4.1_0
  - r-progress=1.1.2=r3.4.1_0
  - r-r6=2.2.1=r3.4.1_0
  - r-rcolorbrewer=1.1_2=r3.4.1_3
  - r-rcpp=0.12.11=r3.4.1_0
  - r-rcpparmadillo=0.7.900.2.0=r3.4.1_0
  - r-rcurl=1.95_4.8=r3.4.1_0
  - r-registry=0.3=r3.4.1_0
  - r-reshape2=1.4.2=r3.4.1_0
  - r-rjson=0.2.15=r3.4.1_0
  - r-rlang=0.1.1=r3.4.1_0
  - r-rmarkdown=1.5=r3.4.1_0
  - r-rngtools=1.2.4=r3.4.1_0
  - r-rpart=4.1_11=r3.4.1_0
  - r-rprojroot=1.2=r3.4.1_0
  - r-rsqlite=1.1_2=r3.4.1_0
  - r-scales=0.4.1=r3.4.1_0
  - r-snow=0.4_2=r3.4.1_0
  - r-stringi=1.1.5=r3.4.1_0
  - r-stringr=1.2.0=r3.4.1_0
  - r-survival=2.41_3=r3.4.1_0
  - r-tibble=1.3.3=r3.4.1_0
  - r-viridis=0.4.0=r3.4.1_0
  - r-viridislite=0.2.0=r3.4.1_0
  - r-xml=3.98_1.7=r3.4.1_0
  - r-xtable=1.8_2=r3.4.1_0
  - r-yaml=2.1.14=r3.4.1_0
  - ratelimiter=1.2.0=py36_0
  - readline=7.0=hb321a52_4
  - regex=2017.09.23=py36h2527052_0
  - requests=2.14.2=py36_0
  - s3transfer=0.1.10=py36h0257dcc_1
  - samtools=1.5=1
  - scikit-learn=0.19.1=py36h7aa7ec6_0
  - scipy=1.0.0=py36hbf646e7_0
  - seaborn=0.8.0=py36h197244f_0
  - seqtk=1.3=hed695b0_2
  - setuptools=36.5.0=py36he42e2e1_0
  - setuptools-git=1.2=py36_0
  - simplegeneric=0.8.1=py36h2cb9092_0
  - simplejson=3.11.1=py36_0
  - sip=4.18.1=py36h51ed4ed_2
  - six=1.11.0=py36h372c433_1
  - snakemake=4.3.0=py36_0
  - sqlite=3.20.1=hb898158_2
  - star=2.6.0c=1
  - statsmodels=0.8.0=py36h8533d0b_0
  - system=5.8=2
  - tbb=2019.8=hc9558a2_0
  - terminado=0.6=py36ha25a19f_0
  - testpath=0.3.1=py36h8cadb63_0
  - tk=8.6.7=hc745277_3
  - toolz=0.9.0=py36_0
  - tornado=4.5.2=py36h1283b2a_0
  - traitlets=4.3.2=py36h674d592_0
  - ucsc-bedclip=377=h199ee4e_0
  - ucsc-bedgraphtobigwig=332=0
  - ucsc-bedtobigbed=332=0
  - ucsc-twobittofa=357=1
  - umi_tools=0.5.1=py36_0
  - urllib3=1.22=py36hbe7ace6_0
  - wcwidth=0.1.7=py36hdf4376a_0
  - webencodings=0.5.1=py36h800622e_1
  - werkzeug=0.12.2=py36hc703753_0
  - wget=1.19.1=he4ec0ba_0
  - wheel=0.29.0=py36he7f4e38_1
  - wrapt=1.10.11=py36h28b7045_0
  - xmltodict=0.11.0=py36_0
  - xopen=0.8.4=py36_0
  - xz=5.2.3=h55aa19d_2
  - yaml=0.1.7=h014fa73_2
  - yarl=0.13.0=py36h21e4b6b_0
  - zeromq=4.2.2=hbedb6e5_2
  - zlib=1.2.11=ha838bed_2
  - pip:
    - pillow==8.3.2
prefix: /home/ec2-user/anaconda3/envs/eclipsebio

Answer 1

乍一看，这种环境可能存在许多问题。一些最明显的事情是：

• 您可能需要将channel_priority设置为flexible，即，

conda配置--设置灵活的channel_priority

否则，优先级较高的通道可能是其他通道中的屏蔽包。

• 通道顺序不符合标准。免费的频道应该总是最后一个，Bioconda有非常具体的频道顺序要求，以确保他们的软件包正常工作。将顺序更改为：

通道：- conda-forge - bioconda - defaults free

• 切换到Mamba。

html_ribo_report.yaml安装基本-n conda-forge::mamba env create -n html_ribo_report -f conda

否则，我会考虑将环境拆分成更模块化(即可管理)的组件，以适应不同的任务。就我个人而言，我避免在同一环境中混合使用Python和R，而将Snakemake放在自己的专用环境中。