linux学习100篇34:转录组分析用软件及安装mutiqc

错了 multiqc 少了l

$ conda install -y mutiqc
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - mutiqc

Current channels:

  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


(rnaseq) root 11:31:28 ~
$ mutiqc
-bash: mutiqc: command not found
(rnaseq) root 11:31:42 ~
$ multiqc
-bash: multiqc: command not found
(rnaseq) root 11:31:54 ~
$ multiqc --help
-bash: multiqc: command not found
(rnaseq) root 11:32:05 ~
$ multiqc -h
-bash: multiqc: command not found
(rnaseq) root 11:32:13 ~
$ 

重来

$ conda install -y multiqc
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /root/miniconda3/envs/rnaseq

  added / updated specs:
    - multiqc


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    brotlipy-0.7.0             |py39h3811e60_1001         341 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    cffi-1.14.5                |   py39he32792d_0         227 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    chardet-4.0.0              |   py39hf3d152e_1         205 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    click-8.0.1                |   py39hf3d152e_0         146 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    colorama-0.4.4             |     pyh9f0ad1d_0          18 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    coloredlogs-15.0           |   py39hf3d152e_0          62 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    colormath-3.0.0            |             py_2          34 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    commonmark-0.9.1           |             py_0          46 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    cryptography-3.4.7         |   py39hbca0aa6_0         1.1 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    cycler-0.10.0              |             py_2           9 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    decorator-4.4.2            |             py_0          11 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    future-0.18.2              |   py39hf3d152e_3         718 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    humanfriendly-9.1          |   py39hf3d152e_0         118 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    idna-2.10                  |     pyh9f0ad1d_0          52 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    importlib-metadata-4.3.1   |   py39hf3d152e_0          30 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    jinja2-3.0.1               |     pyhd8ed1ab_0          99 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    kiwisolver-1.3.1           |   py39h1a9c180_1          80 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libblas-3.9.0              |       9_openblas          11 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libcblas-3.9.0             |       9_openblas          11 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libgfortran-ng-9.3.0       |      hff62375_19          22 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libgfortran5-9.3.0         |      hff62375_19         2.0 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    liblapack-3.9.0            |       9_openblas          11 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libopenblas-0.3.15         |pthreads_h8fe5266_1         9.2 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    lzstring-1.0.4             |          py_1001           6 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    markdown-3.3.4             |     pyhd8ed1ab_0          67 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    markupsafe-2.0.1           |   py39h3811e60_0          22 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    matplotlib-base-3.4.2      |   py39h2fa2bec_0         7.2 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    multiqc-1.10.1             |     pyhdfd78af_1         898 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    networkx-2.5.1             |     pyhd8ed1ab_0         1.2 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    numpy-1.20.3               |   py39hdbf815f_1         5.8 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    olefile-0.46               |     pyh9f0ad1d_1          32 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    openjpeg-2.4.0             |       hb52868f_1         444 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pillow-8.2.0               |   py39hf95b381_1         690 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pycparser-2.20             |     pyh9f0ad1d_2          94 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pygments-2.9.0             |     pyhd8ed1ab_0         754 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pyopenssl-20.0.1           |     pyhd8ed1ab_0          48 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pysocks-1.7.1              |   py39hf3d152e_3          28 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    pyyaml-5.4.1               |   py39h3811e60_0         193 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    requests-2.25.1            |     pyhd3deb0d_0          51 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    rich-10.2.2                |   py39hf3d152e_0         337 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    simplejson-3.17.2          |   py39h3811e60_2         103 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    spectra-0.0.11             |             py_1          19 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    tornado-6.1                |   py39h3811e60_1         646 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    typing_extensions-3.7.4.3  |             py_0          25 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    urllib3-1.26.5             |     pyhd8ed1ab_0          99 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    yaml-0.2.5                 |       h516909a_0          82 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    zipp-3.4.1                 |     pyhd8ed1ab_0          11 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    ------------------------------------------------------------
                                           Total:        33.5 MB

The following NEW packages will be INSTALLED:

  brotlipy           anaconda/cloud/conda-forge/linux-64::brotlipy-0.7.0-py39h3811e60_1001
  cffi               anaconda/cloud/conda-forge/linux-64::cffi-1.14.5-py39he32792d_0
  chardet            anaconda/cloud/conda-forge/linux-64::chardet-4.0.0-py39hf3d152e_1
  click              anaconda/cloud/conda-forge/linux-64::click-8.0.1-py39hf3d152e_0
  colorama           anaconda/cloud/conda-forge/noarch::colorama-0.4.4-pyh9f0ad1d_0
  coloredlogs        anaconda/cloud/conda-forge/linux-64::coloredlogs-15.0-py39hf3d152e_0
  colormath          anaconda/cloud/conda-forge/noarch::colormath-3.0.0-py_2
  commonmark         anaconda/cloud/conda-forge/noarch::commonmark-0.9.1-py_0
  cryptography       anaconda/cloud/conda-forge/linux-64::cryptography-3.4.7-py39hbca0aa6_0
  cycler             anaconda/cloud/conda-forge/noarch::cycler-0.10.0-py_2
  decorator          anaconda/cloud/conda-forge/noarch::decorator-4.4.2-py_0
  future             anaconda/cloud/conda-forge/linux-64::future-0.18.2-py39hf3d152e_3
  humanfriendly      anaconda/cloud/conda-forge/linux-64::humanfriendly-9.1-py39hf3d152e_0
  idna               anaconda/cloud/conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  importlib-metadata anaconda/cloud/conda-forge/linux-64::importlib-metadata-4.3.1-py39hf3d152e_0
  jinja2             anaconda/cloud/conda-forge/noarch::jinja2-3.0.1-pyhd8ed1ab_0
  kiwisolver         anaconda/cloud/conda-forge/linux-64::kiwisolver-1.3.1-py39h1a9c180_1
  libblas            anaconda/cloud/conda-forge/linux-64::libblas-3.9.0-9_openblas
  libcblas           anaconda/cloud/conda-forge/linux-64::libcblas-3.9.0-9_openblas
  libgfortran-ng     anaconda/cloud/conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_19
  libgfortran5       anaconda/cloud/conda-forge/linux-64::libgfortran5-9.3.0-hff62375_19
  liblapack          anaconda/cloud/conda-forge/linux-64::liblapack-3.9.0-9_openblas
  libopenblas        anaconda/cloud/conda-forge/linux-64::libopenblas-0.3.15-pthreads_h8fe5266_1
  lzstring           anaconda/cloud/conda-forge/noarch::lzstring-1.0.4-py_1001
  markdown           anaconda/cloud/conda-forge/noarch::markdown-3.3.4-pyhd8ed1ab_0
  markupsafe         anaconda/cloud/conda-forge/linux-64::markupsafe-2.0.1-py39h3811e60_0
  matplotlib-base    anaconda/cloud/conda-forge/linux-64::matplotlib-base-3.4.2-py39h2fa2bec_0
  multiqc            anaconda/cloud/bioconda/noarch::multiqc-1.10.1-pyhdfd78af_1
  networkx           anaconda/cloud/conda-forge/noarch::networkx-2.5.1-pyhd8ed1ab_0
  numpy              anaconda/cloud/conda-forge/linux-64::numpy-1.20.3-py39hdbf815f_1
  olefile            anaconda/cloud/conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1
  openjpeg           anaconda/cloud/conda-forge/linux-64::openjpeg-2.4.0-hb52868f_1
  pillow             anaconda/cloud/conda-forge/linux-64::pillow-8.2.0-py39hf95b381_1
  pycparser          anaconda/cloud/conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
  pygments           anaconda/cloud/conda-forge/noarch::pygments-2.9.0-pyhd8ed1ab_0
  pyopenssl          anaconda/cloud/conda-forge/noarch::pyopenssl-20.0.1-pyhd8ed1ab_0
  pyparsing          anaconda/cloud/conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  pysocks            anaconda/cloud/conda-forge/linux-64::pysocks-1.7.1-py39hf3d152e_3
  python-dateutil    anaconda/cloud/conda-forge/noarch::python-dateutil-2.8.1-py_0
  pyyaml             anaconda/cloud/conda-forge/linux-64::pyyaml-5.4.1-py39h3811e60_0
  requests           anaconda/cloud/conda-forge/noarch::requests-2.25.1-pyhd3deb0d_0
  rich               anaconda/cloud/conda-forge/linux-64::rich-10.2.2-py39hf3d152e_0
  simplejson         anaconda/cloud/conda-forge/linux-64::simplejson-3.17.2-py39h3811e60_2
  six                anaconda/cloud/conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  spectra            anaconda/cloud/conda-forge/noarch::spectra-0.0.11-py_1
  tornado            anaconda/cloud/conda-forge/linux-64::tornado-6.1-py39h3811e60_1
  typing_extensions  anaconda/cloud/conda-forge/noarch::typing_extensions-3.7.4.3-py_0
  urllib3            anaconda/cloud/conda-forge/noarch::urllib3-1.26.5-pyhd8ed1ab_0
  yaml               anaconda/cloud/conda-forge/linux-64::yaml-0.2.5-h516909a_0
  zipp               anaconda/cloud/conda-forge/noarch::zipp-3.4.1-pyhd8ed1ab_0



Downloading and Extracting Packages
numpy-1.20.3         | 5.8 MB    | ######################################## | 100% 
openjpeg-2.4.0       | 444 KB    | ######################################## | 100% 
rich-10.2.2          | 337 KB    | ######################################## | 100% 
colorama-0.4.4       | 18 KB     | ######################################## | 100% 
cffi-1.14.5          | 227 KB    | ######################################## | 100% 
pyyaml-5.4.1         | 193 KB    | ######################################## | 100% 
olefile-0.46         | 32 KB     | ######################################## | 100% 
markdown-3.3.4       | 67 KB     | ######################################## | 100% 
colormath-3.0.0      | 34 KB     | ######################################## | 100% 
networkx-2.5.1       | 1.2 MB    | ######################################## | 100% 
pyparsing-2.4.7      | 60 KB     | ######################################## | 100% 
yaml-0.2.5           | 82 KB     | ######################################## | 100% 
kiwisolver-1.3.1     | 80 KB     | ######################################## | 100% 
future-0.18.2        | 718 KB    | ######################################## | 100% 
markupsafe-2.0.1     | 22 KB     | ######################################## | 100% 
pycparser-2.20       | 94 KB     | ######################################## | 100% 
jinja2-3.0.1         | 99 KB     | ######################################## | 100% 
python-dateutil-2.8. | 220 KB    | ######################################## | 100% 
matplotlib-base-3.4. | 7.2 MB    | ######################################## | 100% 
simplejson-3.17.2    | 103 KB    | ######################################## | 100% 
urllib3-1.26.5       | 99 KB     | ######################################## | 100% 
decorator-4.4.2      | 11 KB     | ######################################## | 100% 
six-1.16.0           | 14 KB     | ######################################## | 100% 
zipp-3.4.1           | 11 KB     | ######################################## | 100% 
libcblas-3.9.0       | 11 KB     | ######################################## | 100% 
liblapack-3.9.0      | 11 KB     | ######################################## | 100% 
brotlipy-0.7.0       | 341 KB    | ######################################## | 100% 
cryptography-3.4.7   | 1.1 MB    | ######################################## | 100% 
libopenblas-0.3.15   | 9.2 MB    | ######################################## | 100% 
libgfortran5-9.3.0   | 2.0 MB    | ######################################## | 100% 
idna-2.10            | 52 KB     | ######################################## | 100% 
tornado-6.1          | 646 KB    | ######################################## | 100% 
spectra-0.0.11       | 19 KB     | ######################################## | 100% 
libblas-3.9.0        | 11 KB     | ######################################## | 100% 
importlib-metadata-4 | 30 KB     | ######################################## | 100% 
typing_extensions-3. | 25 KB     | ######################################## | 100% 
coloredlogs-15.0     | 62 KB     | ######################################## | 100% 
pyopenssl-20.0.1     | 48 KB     | ######################################## | 100% 
requests-2.25.1      | 51 KB     | ######################################## | 100% 
chardet-4.0.0        | 205 KB    | ######################################## | 100% 
pygments-2.9.0       | 754 KB    | ######################################## | 100% 
multiqc-1.10.1       | 898 KB    | ######################################## | 100% 
cycler-0.10.0        | 9 KB      | ######################################## | 100% 
commonmark-0.9.1     | 46 KB     | ######################################## | 100% 
lzstring-1.0.4       | 6 KB      | ######################################## | 100% 
pysocks-1.7.1        | 28 KB     | ######################################## | 100% 
humanfriendly-9.1    | 118 KB    | ######################################## | 100% 
libgfortran-ng-9.3.0 | 22 KB     | ######################################## | 100% 
click-8.0.1          | 146 KB    | ######################################## | 100% 
pillow-8.2.0         | 690 KB    | ######################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rnaseq) root 11:36:08 ~
$ 

查看

$ multiqc
Usage: multiqc [OPTIONS] 

Error: Missing argument ''.

This is MultiQC v1.10.1

For more help, run 'multiqc --help' or visit http://multiqc.info

(rnaseq) root 11:37:01 ~
$ multiqc --help
Usage: multiqc [OPTIONS] 

  MultiQC aggregates results from bioinformatics analyses across many samples
  into a single report.

  It searches a given directory for analysis logs and compiles a HTML report.
  It's a general use tool, perfect for summarising the output from numerous
  bioinformatics tools.

  To run, supply with one or more directory to scan for analysis results. To
  run here, use 'multiqc .'

  See http://multiqc.info for more details.

  Author: Phil Ewels (http://phil.ewels.co.uk)

Options:
  -f, --force                     Overwrite any existing reports
  -d, --dirs                      Prepend directory to sample names
  -dd, --dirs-depth INTEGER       Prepend [INT] directories to sample names.
                                  Negative number to take from start of path.
  -s, --fullnames                 Do not clean the sample names (leave as full
                                  file name)
  -i, --title TEXT                Report title. Printed as page header, used
                                  for filename if not otherwise specified.
  -b, --comment TEXT              Custom comment, will be printed at the top
                                  of the report.
  -n, --filename TEXT             Report filename. Use 'stdout' to print to
                                  standard out.
  -o, --outdir TEXT               Create report in the specified output
                                  directory.
  -t, --template [default|default_dev|gathered|geo|sections|simple]
                                  Report template to use.
  --tag TEXT                      Use only modules which tagged with this
                                  keyword, eg. RNA
  --view-tags, --view_tags        View the available tags and which modules
                                  they load
  -x, --ignore TEXT               Ignore analysis files (glob expression)
  --ignore-samples TEXT           Ignore sample names (glob expression)
  --ignore-symlinks               Ignore symlinked directories and files
  --sample-names PATH             File containing alternative sample names
  --sample-filters PATH           File containing show/hide patterns for the
                                  report
  -l, --file-list                 Supply a file containing a list of file
                                  paths to be searched, one per row
  -e, --exclude [module name]     Do not use this module. Can specify multiple
                                  times.
  -m, --module [module name]      Use only this module. Can specify multiple
                                  times.
  --data-dir                      Force the parsed data directory to be
                                  created.
  --no-data-dir                   Prevent the parsed data directory from being
                                  created.
  -k, --data-format [tsv|json|yaml]
                                  Output parsed data in a different format.
                                  Default: tsv
  -z, --zip-data-dir              Compress the data directory.
  -p, --export                    Export plots as static images in addition to
                                  the report
  -fp, --flat                     Use only flat plots (static images)
  -ip, --interactive              Use only interactive plots (HighCharts
                                  Javascript)
  --lint                          Use strict linting (validation) to help code
                                  development
  --pdf                           Creates PDF report with 'simple' template.
                                  Requires Pandoc to be installed.
  --no-megaqc-upload              Don't upload generated report to MegaQC,
                                  even if MegaQC options are found
  -c, --config PATH               Specific config file to load, after those in
                                  MultiQC dir / home dir / working dir.
  --cl-config, --cl_config TEXT   Specify MultiQC config YAML on the command
                                  line
  -v, --verbose                   Increase output verbosity.  [x>=0]
  -q, --quiet                     Only show log warnings
  --profile-runtime               Add analysis of how long MultiQC takes to
                                  run to the report
  --no-ansi                       Disable coloured log output
  --version                       Show the version and exit.
  -h, --help                      Show this message and exit.
(rnaseq) root 11:37:12 ~

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