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I'm trying to install the latest version of snakemake from conda into a conda env, following the instructions here. I.e.

conda create -n snakemake -c conda-forge -c bioconda snakemake

However, this seems to only give me the option to install snakemake v5.3.0, while the latest no-arch version on conda is v5.15.0.

Any help greatly appreciated.

Solving environment: done

## Package Plan ##

  environment location: /home/ubuntu/anaconda3/envs/snakemake

  added / updated specs:
    - snakemake


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    aioeasywebdav-2.4.0        |        py36_1000          18 KB  conda-forge
    aiohttp-3.6.2              |   py36h7b6447c_0         544 KB
    appdirs-1.4.3              |   py36h28b3542_0          15 KB
    async-timeout-3.0.1        |           py36_0          12 KB
    attrs-19.3.0               |             py_0          39 KB
    bcrypt-3.1.7               |   py36h7b6447c_0          40 KB
    blas-2.14                  |         openblas          10 KB  conda-forge
    boto3-1.9.66               |           py36_0         105 KB
    botocore-1.12.189          |             py_0         3.4 MB
    datrie-0.8                 |   py36h7b6447c_0         147 KB
    docutils-0.16              |           py36_0         668 KB
    dropbox-9.4.0              |           py36_0         756 KB
    filechunkio-1.6            |           py36_0           7 KB  bioconda
    ftputil-3.2                |           py36_0          85 KB  bioconda
    google-api-core-1.16.0     |           py36_1          86 KB
    googleapis-common-protos-1.51.0|           py36_2          72 KB
    idna_ssl-1.1.0             |           py36_0           7 KB
    importlib_metadata-1.5.0   |           py36_0          48 KB
    jsonschema-3.2.0           |           py36_0          95 KB
    liblapacke-3.8.0           |      14_openblas          10 KB  conda-forge
    multidict-4.7.3            |   py36h7b6447c_0          68 KB
    networkx-2.4               |             py_0         1.2 MB
    numpy-1.17.0               |   py36h99e49ec_0          24 KB  r
    numpy-base-1.17.0          |   py36h2f8d375_0         5.2 MB  r
    pandas-1.0.3               |   py36h0573a6f_0         8.6 MB
    protobuf-3.11.4            |   py36he6710b0_0         635 KB
    psutil-5.7.0               |   py36h7b6447c_0         315 KB
    pygraphviz-1.3.1           |           py36_0         205 KB  bioconda
    pynacl-1.3.0               |   py36h7b6447c_0         1.1 MB
    pyrsistent-0.16.0          |   py36h7b6447c_0          93 KB
    pysftp-0.2.9               |           py36_0          31 KB  bioconda
    ratelimiter-1.2.0          |        py36_1000          12 KB  conda-forge
    rsa-3.1.4                  |           py36_0          87 KB  bioconda
    s3transfer-0.1.13          |           py36_0          79 KB
    snakemake-5.3.0            |           py36_1           4 KB  bioconda
    snakemake-minimal-5.3.0    |           py36_1         280 KB  bioconda
    sqlite-3.31.1              |       h62c20be_1         2.0 MB
    typing_extensions-3.7.4.1  |           py36_0          40 KB
    wrapt-1.12.1               |   py36h7b6447c_1          49 KB
    yarl-1.4.2                 |   py36h7b6447c_0         132 KB
    zipp-2.2.0                 |             py_0          12 KB
    ------------------------------------------------------------
                                           Total:        26.2 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  aioeasywebdav      conda-forge/linux-64::aioeasywebdav-2.4.0-py36_1000
  aiohttp            pkgs/main/linux-64::aiohttp-3.6.2-py36h7b6447c_0
  appdirs            pkgs/main/linux-64::appdirs-1.4.3-py36h28b3542_0
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.3.0-py36_0
  async-timeout      pkgs/main/linux-64::async-timeout-3.0.1-py36_0
  attrs              pkgs/main/noarch::attrs-19.3.0-py_0
  bcrypt             pkgs/main/linux-64::bcrypt-3.1.7-py36h7b6447c_0
  blas               conda-forge/linux-64::blas-2.14-openblas
  boto3              pkgs/main/linux-64::boto3-1.9.66-py36_0
  botocore           pkgs/main/noarch::botocore-1.12.189-py_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0
  cachetools         pkgs/main/noarch::cachetools-3.1.1-py_0
  cairo              pkgs/main/linux-64::cairo-1.14.12-h8948797_3
  certifi            pkgs/main/linux-64::certifi-2020.4.5.1-py36_0
  cffi               pkgs/main/linux-64::cffi-1.14.0-py36h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py36_1003
  configargparse     pkgs/main/noarch::configargparse-1.1-py_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py36h1ba5d50_0
  datrie             pkgs/main/linux-64::datrie-0.8-py36h7b6447c_0
  decorator          pkgs/main/noarch::decorator-4.4.2-py_0
  docutils           pkgs/main/linux-64::docutils-0.16-py36_0
  dropbox            pkgs/main/linux-64::dropbox-9.4.0-py36_0
  expat              pkgs/main/linux-64::expat-2.2.6-he6710b0_0
  filechunkio        bioconda/linux-64::filechunkio-1.6-py36_0
  fontconfig         pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0
  freetype           pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1
  fribidi            pkgs/main/linux-64::fribidi-1.0.5-h7b6447c_0
  ftputil            bioconda/linux-64::ftputil-3.2-py36_0
  gitdb              pkgs/main/noarch::gitdb-4.0.2-py_0
  gitpython          pkgs/main/noarch::gitpython-3.1.1-py_1
  glib               pkgs/main/linux-64::glib-2.63.1-h5a9c865_0
  google-api-core    pkgs/main/linux-64::google-api-core-1.16.0-py36_1
  google-auth        pkgs/main/noarch::google-auth-1.13.1-py_0
  google-cloud-core  pkgs/main/noarch::google-cloud-core-1.3.0-py_0
  google-cloud-stor~ pkgs/main/noarch::google-cloud-storage-1.27.0-py_0
  google-resumable-~ pkgs/main/noarch::google-resumable-media-0.5.0-py_1
  googleapis-common~ pkgs/main/linux-64::googleapis-common-protos-1.51.0-py36_2
  graphite2          pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0
  graphviz           pkgs/main/linux-64::graphviz-2.40.1-h21bd128_2
  harfbuzz           pkgs/main/linux-64::harfbuzz-1.8.8-hffaf4a1_0
  icu                pkgs/main/linux-64::icu-58.2-h9c2bf20_1
  idna               pkgs/main/noarch::idna-2.9-py_1
  idna_ssl           pkgs/main/linux-64::idna_ssl-1.1.0-py36_0
  importlib_metadata pkgs/main/linux-64::importlib_metadata-1.5.0-py36_0
  jinja2             pkgs/main/noarch::jinja2-2.11.1-py_0
  jmespath           pkgs/main/noarch::jmespath-0.9.4-py_0
  jpeg               pkgs/main/linux-64::jpeg-9b-h024ee3a_2
  jsonschema         pkgs/main/linux-64::jsonschema-3.2.0-py36_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libblas            conda-forge/linux-64::libblas-3.8.0-14_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-14_openblas
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  liblapack          conda-forge/linux-64::liblapack-3.8.0-14_openblas
  liblapacke         conda-forge/linux-64::liblapacke-3.8.0-14_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.7-h5ec1e0e_6
  libpng             pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libprotobuf        pkgs/main/linux-64::libprotobuf-3.11.4-hd408876_0
  libsodium          pkgs/main/linux-64::libsodium-1.0.16-h1bed415_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  libtiff            pkgs/main/linux-64::libtiff-4.1.0-h2733197_0
  libuuid            pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2
  libxcb             pkgs/main/linux-64::libxcb-1.13-h1bed415_1
  libxml2            pkgs/main/linux-64::libxml2-2.9.9-hea5a465_1
  markupsafe         pkgs/main/linux-64::markupsafe-1.1.1-py36h7b6447c_0
  multidict          pkgs/main/linux-64::multidict-4.7.3-py36h7b6447c_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_0
  networkx           pkgs/main/noarch::networkx-2.4-py_0
  numpy              r/linux-64::numpy-1.17.0-py36h99e49ec_0
  numpy-base         r/linux-64::numpy-base-1.17.0-py36h2f8d375_0
  openssl            pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
  pandas             pkgs/main/linux-64::pandas-1.0.3-py36h0573a6f_0
  pango              pkgs/main/linux-64::pango-1.42.4-h049681c_0
  paramiko           pkgs/main/noarch::paramiko-2.7.1-py_0
  pcre               pkgs/main/linux-64::pcre-8.43-he6710b0_0
  pip                pkgs/main/linux-64::pip-20.0.2-py36_1
  pixman             pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0
  prettytable        conda-forge/noarch::prettytable-0.7.2-py_3
  protobuf           pkgs/main/linux-64::protobuf-3.11.4-py36he6710b0_0
  psutil             pkgs/main/linux-64::psutil-5.7.0-py36h7b6447c_0
  pyasn1             pkgs/main/noarch::pyasn1-0.4.8-py_0
  pyasn1-modules     pkgs/main/noarch::pyasn1-modules-0.2.7-py_0
  pycparser          pkgs/main/noarch::pycparser-2.20-py_0
  pygraphviz         bioconda/linux-64::pygraphviz-1.3.1-py36_0
  pynacl             pkgs/main/linux-64::pynacl-1.3.0-py36h7b6447c_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py36_0
  pyrsistent         pkgs/main/linux-64::pyrsistent-0.16.0-py36h7b6447c_0
  pysftp             bioconda/linux-64::pysftp-0.2.9-py36_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py36_0
  python             pkgs/main/linux-64::python-3.6.10-hcf32534_1
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.1-py_0
  python-irodsclient conda-forge/noarch::python-irodsclient-0.8.2-py_0
  pytz               pkgs/main/noarch::pytz-2019.3-py_0
  pyyaml             pkgs/main/linux-64::pyyaml-5.3.1-py36h7b6447c_0
  ratelimiter        conda-forge/linux-64::ratelimiter-1.2.0-py36_1000
  readline           pkgs/main/linux-64::readline-8.0-h7b6447c_0
  requests           pkgs/main/linux-64::requests-2.23.0-py36_0
  rsa                bioconda/linux-64::rsa-3.1.4-py36_0
  s3transfer         pkgs/main/linux-64::s3transfer-0.1.13-py36_0
  setuptools         pkgs/main/linux-64::setuptools-46.1.3-py36_0
  six                pkgs/main/linux-64::six-1.14.0-py36_0
  smmap              pkgs/main/noarch::smmap-3.0.2-py_0
  snakemake          bioconda/linux-64::snakemake-5.3.0-py36_1
  snakemake-minimal  bioconda/linux-64::snakemake-minimal-5.3.0-py36_1
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  typing_extensions  pkgs/main/linux-64::typing_extensions-3.7.4.1-py36_0
  urllib3            pkgs/main/linux-64::urllib3-1.25.8-py36_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py36_0
  wrapt              pkgs/main/linux-64::wrapt-1.12.1-py36h7b6447c_1
  xmlrunner          conda-forge/noarch::xmlrunner-1.7.7-py_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  yarl               pkgs/main/linux-64::yarl-1.4.2-py36h7b6447c_0
  zipp               pkgs/main/noarch::zipp-2.2.0-py_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
  zstd               pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0


Proceed ([y]/n)?

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  • 1
    $\begingroup$ Does it help if you include the specific version? conda create -n snakemake -c conda-forge -c bioconda snakemake=5.15 $\endgroup$
    – mrhd
    Apr 27 '20 at 9:33
  • $\begingroup$ @mrhd - yes, it does, thanks for the suggestion $\endgroup$
    – flashton
    Apr 29 '20 at 6:17
4
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This is an example of the conda solver behaving incorrectly. In this case, it's choosing to pick a version that minimizes the number of dependencies required. Version 5.3.0 has 25 fewer dependencies, so if you let conda choose the version that's what it will pick. There's nothing you can really do about this other than specifying the version of snakemake that you want.

Update: It's very likely that mamba will correctly do what you want by default. Though I haven't used it, it's supposed to be a drop in replacement for conda here.

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  • $\begingroup$ That works! Thanks Devon (I'm sure that's one of the things I tried, but perhaps when my channels were still in the wrong order...) $\endgroup$
    – flashton
    Apr 29 '20 at 6:16
  • 1
    $\begingroup$ From next release on, installing via mamba is the default recommendation for Snakemake. $\endgroup$ May 2 '20 at 14:27
  • $\begingroup$ Actually, the issue does not seem to be the number of dependencies, but rather a lack of information in the stripped down current_repodata.json. If that is disabled and conda uses the full repodata, results are correct again, see github.com/conda/conda/issues/9905 $\endgroup$ May 2 '20 at 14:29
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I don't know if it means anything but...

  • It seems you are using anaconda instead of miniconda as required by the snakemake docs. Maybe reinstall conda using miniconda3.

  • conda is installing python 3.6 instead of the more recent 3.8... odd

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  • 1
    $\begingroup$ anaconda is just miniconda with a bunch of additional packages installed. $\endgroup$
    – Devon Ryan
    Apr 28 '20 at 20:45

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