NanoPlot
NanoPlot copied to clipboard
wdecoster
Conda installation
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
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
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
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)?
Well, conda works in mysterious ways? But good to hear things are solved.