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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
407 stars 48 forks source link

Conda installation #294

Closed mike-molnar closed 1 year ago

mike-molnar commented 2 years ago

Hi Wouter,

I was trying to install NanoPlot and NanoFilt with conda, but was having issues. I found that it worked if I installed NanoFilt first, but it took some time for it to install NanoPlot after. It worked, but I had to downgrade two packages that I think were both installed from NanoFilt:

The following packages will be DOWNGRADED:

  matplotlib-base                      3.5.1-py38hf4fb855_0 --> 3.3.2-py38h5c7f4ab_1
  networkx                                 2.8-pyhd8ed1ab_0 --> 2.7.1-pyhd8ed1ab_0

I was able to get it to install, but I thought I should at least raise the issue in case others may have a similar problem.

Best, Mike

wdecoster commented 2 years ago

Hi Mike,

Hm, thanks for reporting this. I don't immediately have a clue what is going on. Is that in a fresh environment? Matplotlib doesn't really have anything to do with NanoFilt, so I don't think that fully explains it. Did you have any error messages that suggested this to be the case? Also, did you use conda or mamba? I would advise the latter, it is a drop-in replacement that is I) faster and ii) usually better at resolving dependencies.

Cheers, Wouter

tchrisboles commented 2 years ago

Wouter, like Mike, I had a bit of trouble updating my NanoPlot installation to the current version using the current conda software. I removed the old NanoPlot package and deleted the env, and reinstalled NanoPlot in fresh new env and everything worked fine. Seems something was wonky updating from old to current NanoPlot package from current conda version. Chris

mike-molnar commented 2 years ago

I was setting up a new environment with nanopolish and medaka to see if they could play nice together on conda. It turns out they do play nice now, so I had those two installed and a handful of others, but I would only get issues with the installation when I included nanoplot and nanofilt.

I tried a fresh install with just nanoplot and nanofilt and there were no issues reported. The odd thing was that I didn't see either of those packages when I did a fresh install with just those two:

  added / updated specs:
    - nanofilt
    - nanoplot

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    arrow-cpp-0.11.1           |   py36h3bd774a_0         6.1 MB  conda-forge
    biopython-1.79             |   py36h8f6f2f9_0         2.7 MB  conda-forge
    boost-cpp-1.68.0           |    h11c811c_1000        20.5 MB  conda-forge
    certifi-2016.9.26          |           py36_0         217 KB  conda-forge
    kaleido-core-0.2.1         |       h3644ca4_0        59.2 MB  conda-forge
    mathjax-2.7.7              |                0        21.3 MB  conda-forge
    nanoplot-1.40.0            |     pyhdfd78af_0          42 KB  bioconda
    nss-3.77                   |       h2350873_0         2.1 MB  conda-forge
    numpy-1.19.5               |   py36hfc0c790_2         5.3 MB  conda-forge
    pandas-1.1.5               |   py36h284efc9_0        11.3 MB  conda-forge
    parquet-cpp-1.5.1          |                3           3 KB  conda-forge
    pip-20.0.2                 |           py36_1         1.9 MB  conda-forge
    pyarrow-0.11.1             |py36hbbcf98d_1002         1.9 MB  conda-forge
    pysam-0.19.0               |   py36hea1697a_0         2.6 MB  bioconda
    python-3.6.15              |hb7a2778_0_cpython        38.4 MB  conda-forge
    python-kaleido-0.2.1       |     pyhd8ed1ab_0          18 KB  conda-forge
    python_abi-3.6             |          2_cp36m           4 KB  conda-forge
    scipy-1.5.3                |   py36h81d768a_1        19.1 MB  conda-forge
    setuptools-49.6.0          |   py36h5fab9bb_3         936 KB  conda-forge
    wrapt-1.12.1               |   py36h8f6f2f9_3          47 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       193.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  arrow-cpp          conda-forge/linux-64::arrow-cpp-0.11.1-py36h3bd774a_0
  biopython          conda-forge/linux-64::biopython-1.79-py36h8f6f2f9_0
  boost-cpp          conda-forge/linux-64::boost-cpp-1.68.0-h11c811c_1000
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  c-ares             conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2021.10.8-ha878542_0
  certifi            conda-forge/linux-64::certifi-2016.9.26-py36_0
  deprecated         conda-forge/noarch::deprecated-1.2.13-pyh6c4a22f_0
  expat              conda-forge/linux-64::expat-2.4.8-h27087fc_0
  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0
  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0
  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-hab24e00_0
  fontconfig         conda-forge/linux-64::fontconfig-2.14.0-h8e229c2_0
  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0
  freetype           conda-forge/linux-64::freetype-2.10.4-h0708190_1
  icu                conda-forge/linux-64::icu-58.2-hf484d3e_1000
  kaleido-core       conda-forge/linux-64::kaleido-core-0.2.1-h3644ca4_0
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.19.3-h3790be6_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
  libblas            conda-forge/linux-64::libblas-3.9.0-14_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-14_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-7.82.0-h7bff187_0
  libdeflate         conda-forge/linux-64::libdeflate-1.10-h7f98852_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-11.2.0-h1d223b6_15
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_15
  libgfortran5       conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_15
  libgomp            conda-forge/linux-64::libgomp-11.2.0-h1d223b6_15
  liblapack          conda-forge/linux-64::liblapack-3.9.0-14_linux64_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.47.0-h727a467_0
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
  libopenblas        conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
  libpng             conda-forge/linux-64::libpng-1.6.37-h21135ba_2
  libssh2            conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-11.2.0-he4da1e4_15
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
  libzlib            conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
  mathjax            conda-forge/linux-64::mathjax-2.7.7-0
  nanofilt           bioconda/noarch::nanofilt-2.8.0-py_0
  nanoget            bioconda/noarch::nanoget-1.16.1-py_0
  nanomath           bioconda/noarch::nanomath-1.2.1-pyhdfd78af_0
  nanoplot           bioconda/noarch::nanoplot-1.40.0-pyhdfd78af_0
  ncurses            conda-forge/linux-64::ncurses-6.3-h27087fc_1
  nspr               conda-forge/linux-64::nspr-4.32-h9c3ff4c_1
  nss                conda-forge/linux-64::nss-3.77-h2350873_0
  numpy              conda-forge/linux-64::numpy-1.19.5-py36hfc0c790_2
  openssl            conda-forge/linux-64::openssl-1.1.1n-h166bdaf_0
  pandas             conda-forge/linux-64::pandas-1.1.5-py36h284efc9_0
  parquet-cpp        conda-forge/noarch::parquet-cpp-1.5.1-3
  pip                conda-forge/linux-64::pip-20.0.2-py36_1
  plotly             conda-forge/noarch::plotly-5.7.0-pyhd8ed1ab_0
  pyarrow            conda-forge/linux-64::pyarrow-0.11.1-py36hbbcf98d_1002
  pysam              bioconda/linux-64::pysam-0.19.0-py36hea1697a_0
  python             conda-forge/linux-64::python-3.6.15-hb7a2778_0_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python-kaleido     conda-forge/noarch::python-kaleido-0.2.1-pyhd8ed1ab_0
  python_abi         conda-forge/linux-64::python_abi-3.6-2_cp36m
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  readline           conda-forge/linux-64::readline-8.1-h46c0cb4_0
  scipy              conda-forge/linux-64::scipy-1.5.3-py36h81d768a_1
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py36h5fab9bb_3
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  sqlite             conda-forge/linux-64::sqlite-3.38.2-h4ff8645_0
  tenacity           conda-forge/noarch::tenacity-8.0.1-pyhd8ed1ab_0
  tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0
  wheel              conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
  wrapt              conda-forge/linux-64::wrapt-1.12.1-py36h8f6f2f9_3
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h166bdaf_1014

Proceed ([y]/n)?
wdecoster commented 2 years ago

Well, conda works in mysterious ways? But good to hear things are solved.