我遇到了一个问题，我的conda环境不是从.yaml文件创建的。我认为它失败了，因为这个yaml文件是在centos6上创建的，但是我已经在AWS上升级到新的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(大约需要一个小时运行)。如果需要，我可以粘贴输出。
html_ribo_report.yaml的内容如下:
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
乍一看，这个环境可能存在许多问题。一些最明显的事情是:
-
您可能需要channel_priority设置为
flexible，即conda config --set channel_priority flexible否则，高优先级通道可能会屏蔽其他通道中的包。
-
通道订单不合格。通道应该总是放在最后，Bioconda有非常具体的通道顺序要求，以确保他们的封装工作。将顺序改为:
channels: - conda-forge - bioconda - defaults - free -
切换到曼巴
conda install -n base conda-forge::mamba mamba env create -n html_ribo_report -f html_ribo_report.yaml
否则，我会考虑将环境分解为适合不同任务的更模块化(即可管理的)组件。就我个人而言，我避免在同一个环境中混合使用Python和R，并将Snakemake保留在自己的专用环境中。