ModuleNotFoundError: No module named 'contextvars'

nick-youngblut commented 2 years ago

Short description of the problem

Conda install (anvio 7 hdfd78af_1 bionconda) on Ubuntu 18.04.6 produces the following error:

$ anvi-self-test --suite mini
Traceback (most recent call last):
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/summaryhtml.py", line 18, in <module>
    from django.conf import settings
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/conf/__init__.py", line 19, in <module>
    from django.utils.deprecation import RemovedInDjango50Warning
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/utils/deprecation.py", line 5, in <module>
    from asgiref.sync import sync_to_async
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/asgiref/sync.py", line 2, in <module>
    import contextvars
ModuleNotFoundError: No module named 'contextvars'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/bin/anvi-self-test", line 91, in <module>
    from anvio.argparse import ArgumentParser
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/argparse.py", line 15, in <module>
    from anvio.programs import Program
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/programs.py", line 21, in <module>
    from anvio.summaryhtml import SummaryHTMLOutput
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/summaryhtml.py", line 49, in <module>
    raise ConfigError('You need to have Django module (http://djangoproject.com) installed on your system to generate HTML output.')
anvio.errors.ConfigError:

Config Error: You need to have Django module (http://djangoproject.com) installed on your
              system to generate HTML output.

Other commands (eg., anvi-migrate) generate the same error.

django is already installed in my conda env: django 4.0 pyhd8ed1ab_0 conda-forge

Creation of the conda env: mamba create -n anvio_env bioconda::anvio

anvi'o version

Anvi'o .......................................: hope (v7)

Profile database .............................: 35
Contigs database .............................: 20
Pan database .................................: 14
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 1

System info

Ubuntu 18.04.6

Conda env

# packages in environment at /tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
anvio                     7                    hdfd78af_1    bioconda
anvio-minimal             7                          py_0    bioconda
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
asgiref                   3.5.0              pyhd8ed1ab_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_9    conda-forge
bioconductor-qvalue       2.26.0            r41hdfd78af_0    bioconda
biopython                 1.79             py36h8f6f2f9_0    conda-forge
blast                     2.12.0               hf3cf87c_4    bioconda
blast-legacy              2.2.26               h9ee0642_3    bioconda
boost-cpp                 1.74.0               h6cacc03_7    conda-forge
bottle                    0.12.18                    py_0    conda-forge
bowtie2                   2.4.5            py36hfca12d5_2    bioconda
brotlipy                  0.7.0           py36h8f6f2f9_1001    conda-forge
bwa                       0.7.17               h7132678_9    bioconda
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cairo                     1.16.0            ha12eb4b_1010    conda-forge
centrifuge                1.0.4_beta      py36pl526he941832_2    bioconda
certifi                   2021.5.30        py36h5fab9bb_0    conda-forge
cffi                      1.14.6           py36hd8eec40_1    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
colored                   1.4.2                      py_0    conda-forge
configargparse            1.5.3              pyhd8ed1ab_0    conda-forge
cryptography              35.0.0           py36hb60f036_0    conda-forge
curl                      7.82.0               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
datrie                    0.8.2            py36h8f6f2f9_2    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
diamond                   2.0.14               hb97b32f_1    bioconda
django                    4.0                pyhd8ed1ab_0    conda-forge
docutils                  0.17.1           py36h5fab9bb_0    conda-forge
entrez-direct             16.2                 he881be0_0    bioconda
ete3                      3.1.2              pyh9f0ad1d_0    conda-forge
expat                     2.4.8                h27087fc_0    conda-forge
fastani                   1.33                 h0fdf51a_0    bioconda
fasttree                  2.1.11               hec16e2b_1    bioconda
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               h8e229c2_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gcc_impl_linux-64         10.3.0              hf2f2afa_15    conda-forge
gcc_linux-64              10.3.0               hc39de41_9    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
gfortran_impl_linux-64    10.3.0              h73f4979_15    conda-forge
gfortran_linux-64         10.3.0               hb09a455_9    conda-forge
gitdb                     4.0.9              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.18             pyhd8ed1ab_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.20.1               hcf0ee16_1    conda-forge
gstreamer                 1.20.1               hd4edc92_1    conda-forge
gxx_impl_linux-64         10.3.0              hf2f2afa_15    conda-forge
gxx_linux-64              10.3.0               h2593f52_9    conda-forge
harfbuzz                  4.2.0                h40b6f09_0    conda-forge
hmmer                     3.3.2                h87f3376_2    bioconda
htslib                    1.15.1               h9753748_0    bioconda
icu                       69.1                 h9c3ff4c_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
illumina-utils            2.12               pyhdfd78af_0    bioconda
importlib-metadata        4.8.1            py36h5fab9bb_0    conda-forge
infernal                  1.1.4                h779adbc_0    bioconda
ipython_genutils          0.2.0                      py_1    conda-forge
iqtree                    2.2.0_beta           hb97b32f_1    bioconda
jbig                      2.1               h7f98852_2003    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
jsonschema                4.1.2              pyhd8ed1ab_0    conda-forge
jupyter_core              4.8.1            py36h5fab9bb_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.3.1            py36h605e78d_1    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           14_linux64_openblas    conda-forge
libcblas                  3.9.0           14_linux64_openblas    conda-forge
libclang                  13.0.1          default_hc23dcda_0    conda-forge
libcurl                   7.82.0               h7bff187_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     10.3.0              he6cfe16_15    conda-forge
libgcc-ng                 11.2.0              h1d223b6_15    conda-forge
libgfortran-ng            11.2.0              h69a702a_15    conda-forge
libgfortran5              11.2.0              h5c6108e_15    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   11.2.0              h1d223b6_15    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           14_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libllvm13                 13.0.1               hf817b99_2    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.20          pthreads_h78a6416_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     14.2                 hd57d9b9_0    conda-forge
libsanitizer              10.3.0              h26c7422_15    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-devel_linux-64  10.3.0              he6cfe16_15    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_15    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h885dcf4_1    conda-forge
libxslt                   1.1.33               h0ef7038_3    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
llvm-openmp               8.0.1                hc9558a2_0    conda-forge
llvmlite                  0.36.0           py36h05121d2_0    conda-forge
lxml                      4.6.3            py36h04a5ba7_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
matplotlib-base           3.3.4            py36hd391965_0    conda-forge
mcl                       14.137          pl5262h779adbc_6    bioconda
megahit                   1.2.9                h2e03b76_1    bioconda
mistune                   2.0.2              pyhd8ed1ab_0    conda-forge
mummer                    3.23            pl5262h1b792b2_12    bioconda
muscle                    5.1                  h9f5acd7_1    bioconda
mysql-common              8.0.28               haf5c9bc_3    conda-forge
mysql-libs                8.0.28               h28c427c_3    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.77                 h2350873_0    conda-forge
numba                     0.53.1           py36h1328434_1    conda-forge
numpy                     1.19.5           py36hfc0c790_2    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openmp                    8.0.1                         0    conda-forge
openssl                   1.1.1n               h166bdaf_0    conda-forge
pandas                    0.25.1           py36hb3f55d8_0    conda-forge
pandoc                    2.17.1.1             ha770c72_0    conda-forge
pango                     1.50.6               hbd2fdc8_0    conda-forge
paste                     3.5.0              pyh9f0ad1d_0    conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.37                h032f7d1_0    conda-forge
perl                      5.26.2            h36c2ea0_1008    conda-forge
perl-archive-tar          2.32                    pl526_0    bioconda
perl-carp                 1.38                    pl526_3    bioconda
perl-common-sense         3.74                    pl526_2    bioconda
perl-compress-raw-bzip2   2.087           pl526he1b5a44_0    bioconda
perl-compress-raw-zlib    2.087           pl526hc9558a2_0    bioconda
perl-exporter             5.72                    pl526_1    bioconda
perl-exporter-tiny        1.002001                pl526_0    bioconda
perl-extutils-makemaker   7.36                    pl526_1    bioconda
perl-io-compress          2.087           pl526he1b5a44_0    bioconda
perl-io-zlib              1.10                    pl526_2    bioconda
perl-json                 4.02                    pl526_0    bioconda
perl-json-xs              2.34            pl526h6bb024c_3    bioconda
perl-list-moreutils       0.428                   pl526_1    bioconda
perl-list-moreutils-xs    0.428                   pl526_0    bioconda
perl-pathtools            3.75            pl526h14c3975_1    bioconda
perl-scalar-list-utils    1.52            pl526h516909a_0    bioconda
perl-types-serialiser     1.0                     pl526_2    bioconda
perl-xsloader             0.24                    pl526_0    bioconda
pillow                    8.3.2            py36h676a545_0    conda-forge
pip                       21.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
prodigal                  2.6.3                hec16e2b_4    bioconda
psutil                    5.4.3                    py36_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyani                     0.2.10                     py_0    bioconda
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyqt                      5.12.3           py36h5fab9bb_7    conda-forge
pyqt-impl                 5.12.3           py36h7ec31b9_7    conda-forge
pyqt5-sip                 4.19.18          py36hc4f0c31_7    conda-forge
pyqtchart                 5.12             py36h7ec31b9_7    conda-forge
pyqtwebengine             5.12.1           py36h7ec31b9_7    conda-forge
pyrsistent                0.17.3           py36h8f6f2f9_2    conda-forge
pysam                     0.19.0           py36hea1697a_0    bioconda
pysocks                   1.7.1            py36h5fab9bb_3    conda-forge
python                    3.6.15          hb7a2778_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-levenshtein        0.12.2           py36h8f6f2f9_0    conda-forge
python_abi                3.6                     2_cp36m    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py36h8f6f2f9_1    conda-forge
qt                        5.12.9               h1304e3e_6    conda-forge
r-askpass                 1.1               r41hcfec24a_2    conda-forge
r-assertthat              0.2.1             r41hc72bb7e_2    conda-forge
r-backports               1.4.1             r41hcfec24a_0    conda-forge
r-base                    4.1.3                hd930d0e_0    conda-forge
r-base64enc               0.1_3           r41hcfec24a_1004    conda-forge
r-bit                     4.0.4             r41hcfec24a_0    conda-forge
r-bit64                   4.0.5             r41hcfec24a_0    conda-forge
r-blob                    1.2.2             r41hc72bb7e_0    conda-forge
r-brio                    1.1.3             r41hcfec24a_0    conda-forge
r-broom                   0.7.12            r41hc72bb7e_0    conda-forge
r-bslib                   0.3.1             r41hc72bb7e_0    conda-forge
r-callr                   3.7.0             r41hc72bb7e_0    conda-forge
r-cellranger              1.1.0           r41hc72bb7e_1004    conda-forge
r-cli                     3.2.0             r41h03ef668_0    conda-forge
r-clipr                   0.8.0             r41hc72bb7e_0    conda-forge
r-colorspace              2.0_3             r41h06615bd_0    conda-forge
r-cpp11                   0.4.2             r41hc72bb7e_0    conda-forge
r-crayon                  1.5.1             r41hc72bb7e_0    conda-forge
r-curl                    4.3.2             r41hcfec24a_0    conda-forge
r-data.table              1.14.2            r41hcfec24a_0    conda-forge
r-dbi                     1.1.2             r41hc72bb7e_0    conda-forge
r-dbplyr                  2.1.1             r41hc72bb7e_0    conda-forge
r-desc                    1.4.1             r41hc72bb7e_0    conda-forge
r-diffobj                 0.3.5             r41hcfec24a_0    conda-forge
r-digest                  0.6.29            r41h03ef668_0    conda-forge
r-dplyr                   1.0.8             r41h7525677_0    conda-forge
r-dtplyr                  1.2.1             r41hc72bb7e_0    conda-forge
r-ellipsis                0.3.2             r41hcfec24a_0    conda-forge
r-evaluate                0.15              r41hc72bb7e_0    conda-forge
r-fansi                   1.0.3             r41h06615bd_0    conda-forge
r-farver                  2.1.0             r41h03ef668_0    conda-forge
r-fastmap                 1.1.0             r41h03ef668_0    conda-forge
r-forcats                 0.5.1             r41hc72bb7e_0    conda-forge
r-fs                      1.5.2             r41h7525677_1    conda-forge
r-gargle                  1.2.0             r41hc72bb7e_0    conda-forge
r-generics                0.1.2             r41hc72bb7e_0    conda-forge
r-getopt                  1.20.3            r41ha770c72_2    conda-forge
r-ggplot2                 3.3.5             r41hc72bb7e_0    conda-forge
r-glue                    1.6.2             r41h06615bd_0    conda-forge
r-googledrive             2.0.0             r41hc72bb7e_0    conda-forge
r-googlesheets4           1.0.0             r41h785f33e_0    conda-forge
r-gtable                  0.3.0             r41hc72bb7e_3    conda-forge
r-haven                   2.4.3             r41h2713e49_0    conda-forge
r-highr                   0.9               r41hc72bb7e_0    conda-forge
r-hms                     1.1.1             r41hc72bb7e_0    conda-forge
r-htmltools               0.5.2             r41h03ef668_0    conda-forge
r-httr                    1.4.2             r41hc72bb7e_0    conda-forge
r-ids                     1.0.1             r41hc72bb7e_1    conda-forge
r-isoband                 0.2.5             r41h03ef668_0    conda-forge
r-jquerylib               0.1.4             r41hc72bb7e_0    conda-forge
r-jsonlite                1.8.0             r41h06615bd_0    conda-forge
r-knitr                   1.38              r41hc72bb7e_0    conda-forge
r-labeling                0.4.2             r41hc72bb7e_1    conda-forge
r-lattice                 0.20_45           r41hcfec24a_0    conda-forge
r-lifecycle               1.0.1             r41hc72bb7e_0    conda-forge
r-lubridate               1.8.0             r41h03ef668_0    conda-forge
r-magrittr                2.0.3             r41h06615bd_0    conda-forge
r-mass                    7.3_56            r41h06615bd_0    conda-forge
r-matrix                  1.4_1             r41h0154571_0    conda-forge
r-mgcv                    1.8_40            r41h0154571_0    conda-forge
r-mime                    0.12              r41hcfec24a_0    conda-forge
r-modelr                  0.1.8             r41hc72bb7e_0    conda-forge
r-munsell                 0.5.0           r41hc72bb7e_1004    conda-forge
r-nlme                    3.1_157           r41h8da6f51_0    conda-forge
r-openssl                 2.0.0             r41hfaab4ff_0    conda-forge
r-optparse                1.7.1             r41hc72bb7e_0    conda-forge
r-pillar                  1.7.0             r41hc72bb7e_0    conda-forge
r-pkgconfig               2.0.3             r41hc72bb7e_1    conda-forge
r-pkgload                 1.2.4             r41h03ef668_0    conda-forge
r-plyr                    1.8.7             r41h7525677_0    conda-forge
r-praise                  1.0.0           r41hc72bb7e_1005    conda-forge
r-prettyunits             1.1.1             r41hc72bb7e_1    conda-forge
r-processx                3.5.3             r41h06615bd_0    conda-forge
r-progress                1.2.2             r41hc72bb7e_2    conda-forge
r-ps                      1.6.0             r41hcfec24a_0    conda-forge
r-purrr                   0.3.4             r41hcfec24a_1    conda-forge
r-r6                      2.5.1             r41hc72bb7e_0    conda-forge
r-rappdirs                0.3.3             r41hcfec24a_0    conda-forge
r-rcolorbrewer            1.1_3             r41h785f33e_0    conda-forge
r-rcpp                    1.0.8.3           r41h7525677_0    conda-forge
r-readr                   2.1.2             r41h03ef668_0    conda-forge
r-readxl                  1.4.0             r41hf23e330_0    conda-forge
r-rematch                 1.0.1           r41hc72bb7e_1004    conda-forge
r-rematch2                2.1.2             r41hc72bb7e_1    conda-forge
r-reprex                  2.0.1             r41hc72bb7e_0    conda-forge
r-reshape2                1.4.4             r41h03ef668_1    conda-forge
r-rlang                   1.0.2             r41h7525677_0    conda-forge
r-rmarkdown               2.13              r41hc72bb7e_1    conda-forge
r-rprojroot               2.0.3             r41hc72bb7e_0    conda-forge
r-rstudioapi              0.13              r41hc72bb7e_0    conda-forge
r-rvest                   1.0.2             r41hc72bb7e_0    conda-forge
r-sass                    0.4.1             r41h7525677_0    conda-forge
r-scales                  1.1.1             r41hc72bb7e_0    conda-forge
r-selectr                 0.4_2             r41hc72bb7e_1    conda-forge
r-stringi                 1.7.6             r41h337692f_1    conda-forge
r-stringr                 1.4.0             r41hc72bb7e_2    conda-forge
r-sys                     3.4               r41hcfec24a_0    conda-forge
r-testthat                3.1.3             r41h7525677_0    conda-forge
r-tibble                  3.1.6             r41hcfec24a_0    conda-forge
r-tidyr                   1.2.0             r41h03ef668_0    conda-forge
r-tidyselect              1.1.2             r41hc72bb7e_0    conda-forge
r-tidyverse               1.3.1             r41hc72bb7e_0    conda-forge
r-tinytex                 0.38              r41hc72bb7e_0    conda-forge
r-tzdb                    0.3.0             r41h7525677_0    conda-forge
r-utf8                    1.2.2             r41hcfec24a_0    conda-forge
r-uuid                    1.0_4             r41h06615bd_0    conda-forge
r-vctrs                   0.4.0             r41h7525677_0    conda-forge
r-viridislite             0.4.0             r41hc72bb7e_0    conda-forge
r-vroom                   1.5.7             r41h03ef668_0    conda-forge
r-waldo                   0.4.0             r41hc72bb7e_0    conda-forge
r-withr                   2.5.0             r41hc72bb7e_0    conda-forge
r-xfun                    0.30              r41h7525677_0    conda-forge
r-xml2                    1.3.3             r41h03ef668_0    conda-forge
r-yaml                    2.3.5             r41h06615bd_0    conda-forge
ratelimiter               1.2.0                   py_1002    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
samtools                  1.15.1               h1170115_0    bioconda
scikit-learn              0.20.3           py36ha8026db_1    conda-forge
scipy                     1.5.3            py36h81d768a_1    conda-forge
seaborn                   0.11.2               hd8ed1ab_0    conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
setuptools                58.0.4           py36h5fab9bb_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snakemake-minimal         5.10.0                     py_0    bioconda
spades                    3.14.1               h95f258a_2    bioconda
sqlite                    3.37.1               h4ff8645_0    conda-forge
sqlparse                  0.4.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.12.2           py36he33b4a0_0    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tabulate                  0.8.9              pyhd8ed1ab_0    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
toposort                  1.7                pyhd8ed1ab_0    conda-forge
tornado                   6.1              py36h8f6f2f9_1    conda-forge
traitlets                 4.3.3              pyhd8ed1ab_2    conda-forge
trimal                    1.4.1                h9f5acd7_6    bioconda
trnascan-se               2.0.9           pl5262h779adbc_1    bioconda
typing_extensions         4.1.1              pyha770c72_0    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
wrapt                     1.13.1           py36h8f6f2f9_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxt                1.2.1                h7f98852_2    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zipp                      3.6.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

nick-youngblut commented 2 years ago

Installing contextvars AND zoneinfo (mamba install conda-forge::contextvars conda-forge::backports.zoneinfo) seems to be moving the needle closer:

$ anvi-self-test --suite mini
Traceback (most recent call last):
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/bin/anvi-self-test", line 91, in <module>
    from anvio.argparse import ArgumentParser
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/argparse.py", line 15, in <module>
    from anvio.programs import Program
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/programs.py", line 21, in <module>
    from anvio.summaryhtml import SummaryHTMLOutput
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/anvio/summaryhtml.py", line 53, in <module>
    django.setup()
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/__init__.py", line 16, in setup
    from django.urls import set_script_prefix
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/urls/__init__.py", line 1, in <module>
    from .base import (
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/urls/base.py", line 8, in <module>
    from .exceptions import NoReverseMatch, Resolver404
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/urls/exceptions.py", line 1, in <module>
    from django.http import Http404
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/http/__init__.py", line 5, in <module>
    from django.http.response import (
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/http/response.py", line 16, in <module>
    from django.core.serializers.json import DjangoJSONEncoder
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/core/serializers/__init__.py", line 23, in <module>
    from django.core.serializers.base import SerializerDoesNotExist
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/core/serializers/base.py", line 8, in <module>
    from django.db import models
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/db/models/__init__.py", line 3, in <module>
    from django.db.models.aggregates import *  # NOQA
  File "/tmp/global2/nyoungblut/code/dev/tmp/anvio/conda_envs/anvio/lib/python3.6/site-packages/django/db/models/aggregates.py", line 63
    if (default := c.default) is None:
                ^
SyntaxError: invalid syntax

Relevant updates to the conda env

# Name                    Version                   Build  Channel
contextvars               2.4                        py_0    conda-forge
backports.zoneinfo        0.2.1            py36h8f6f2f9_4    conda-forge

nick-youngblut commented 2 years ago

I could create a github action for testing the conda install (both conda install anvio and the longer install instructions) if you'd accept the PR.

meren commented 2 years ago

Hey @nick-youngblut, thank you very much for the report. We gave up on the conda package for anvi'o a while ago due to tremendously long install times. So it is no surprise the conda package for v7.1 no longer works :/

The official installation instructions for anvi'o online work, but I can see the disadvantage of not having working conda packages for anvi'o :/

Well, we would accept any PR from you with pleasure!!! Thank you very much for your interest and willingness to take a stab at this. But there is something I'd like to bring to your attention first before you invest any time into this:

Just today I realized that we can no longer avoid a switch from Python 3.6 to 3.10 for anvi'o (#1911). Which will be a bit painful, and I don't know the extent of work it will require but I plan to do it ASAP. But if you think what you plan to do would be a waste of time if I were to change the installation instructions (i.e., the Python version, versions of conda and/or Python packages, etc), then I'd suggest you to wait a little longer if you wish.

Best wishes,

nick-youngblut commented 2 years ago

We gave up on the conda package for anvi'o a while ago due to tremendously long install times

This is where mamba really helps. It might be useful to encourage users to switch to mamba for the install instructions, given all of the deps.

Changing the github workflow after your update from python=3.6 to python=3.10 should be rather easy. More generally, adding CI to the anvio repo could help you spot errors during your 3.6 => 3.10 update.

meren commented 2 years ago

This is where mamba really helps.

Yes, but it was also not working for previous versions of anvi'o. We never were able to go after why it was not working.

More generally, adding CI to the anvio repo could help you spot errors during your 3.6 => 3.10 update.

I have no experience with CI so far, but I know it is a critical tool that can help us spot issues early on. So we would be happy for any suggestions and/or guidance if someone were to take it on and run with it.

Best wishes,

nick-youngblut commented 2 years ago

I have no experience with CI so far, but I know it is a critical tool that can help us spot issues early on. So we would be happy for any suggestions and/or guidance if someone were to take it on and run with it.

It's gotten easier with github actions versus travis-ci or circle-ci. My PR would just consist of a quickly modified version of one of my existing workflows. Maybe also a pypi publish workflow

Any reason why you have:

conda install -y -c bioconda "sqlite >=3.31.1"
conda install -y -c bioconda prodigal
conda install -y -c bioconda mcl
conda install -y -c bioconda muscle=3.8.1551
conda install -y -c bioconda hmmer
conda install -y -c bioconda diamond
conda install -y -c bioconda blast
conda install -y -c bioconda megahit
conda install -y -c bioconda spades
conda install -y -c bioconda bowtie2 tbb=2019.8
conda install -y -c bioconda bwa
conda install -y -c bioconda samtools=1.9
conda install -y -c bioconda centrifuge
conda install -y -c bioconda trimal
conda install -y -c bioconda iqtree
conda install -y -c bioconda trnascan-se
conda install -y -c bioconda r-base
conda install -y -c bioconda r-stringi
conda install -y -c bioconda r-tidyverse
conda install -y -c bioconda r-magrittr
conda install -y -c bioconda r-optparse
conda install -y -c bioconda bioconductor-qvalue
conda install -y -c bioconda fasttree

instead of just:

conda install -y -c bioconda "sqlite >=3.31.1" prodigal mcl muscle=3.8.1551 hmmer diamond blast megahit spades bowtie2 tbb=2019.8 bwa samtools=1.9 centrifuge trimal iqtree trnascan-se r-base r-stringi r-tidyverse r-magrittr r-optparse bioconductor-qvalue fasttree
# or mamba install

If any of the recipes fails to install, conda will point out the particular failed dep.

meren commented 2 years ago

During my tests the dependency resolver was taking MUCH longer than what would be the total amount of time for individual steps. I'd be happy to be proven wrong about it.

nick-youngblut commented 2 years ago

During my tests the dependency resolver was taking MUCH longer than what would be the total amount of time for individual steps. I'd be happy to be proven wrong about it.

On my system, mamba took ~13 minutes for mamba install -y -c bioconda "sqlite >=3.31.1" prodigal mcl muscle=3.8.1551 hmmer diamond blast megahit spades bowtie2 tbb=2019.8 bwa samtools=1.9 centrifuge trimal iqtree trnascan-se r-base r-stringi r-tidyverse r-magrittr r-optparse bioconductor-qvalue fasttree

It's the downside of creating an all-in-one toolset instead of multiple modular package (e.g., tidyverse as 1 package versus tidyverse representing many individual packages). I'm guessing that modularizing anvio would probably take too much work at this point. At least mamba can help speed up the install of the long dependency list.

meren commented 2 years ago

Still longer than individual installations with conda, but this is very promising given the added bonus of resolving a lot of headaches in one go.

nick-youngblut commented 2 years ago

PR with a github workflow for CI: https://github.com/merenlab/anvio/pull/1913

jolespin commented 1 year ago

I'm also getting this error from the bioconda installation. How can I get this working? I just downloaded the Delmont 2018 genomes but they are all in CONTIGS.db and CONTIGS.h5 which I can't use. I need fasta format. I'm getting the contextvars install error but when I installed contextvars it dropped my python version down to a version that doesn't have walrus operators.

meren commented 1 year ago

Hey @jolespin, you shouldn't install anvi'o from bioconda. I'm not sure why you went to that rabbit hole. If you follow the installation instructions on anvio.org things should work out just fine. Then anvi-migrate will migrate those old databases to the latest version, and anvi-export-contigs will give you FASTA files.

jolespin commented 1 year ago

Ok awesome, I'll try it out right now! Once I get it working I'll post the conda environment here that might be useful.

jolespin commented 1 year ago

Hopefully this will be helpful for someone.

mamba create -n anvio_env python=3.6
conda activate anvio_env # my mamba init is broken
mamba install -c bioconda 'sqlite>=3.31.1' prodigal mcl muscle=3.8.1551 hmmer diamond blast megahit spades bowtie2 bwa samtools=1.9 centrifuge trimal iqtree trnascan-se r-base r-stringi r-tidyverse r-magrittr r-optparse bioconductor-qvalue fasttree vmatch

Somebody can just use the yml file to recreate the environment quicker:

Call it anvio-dependencies.yml:

name: anvio_env
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_13
  - binutils_impl_linux-64=2.36.1=h193b22a_2
  - binutils_linux-64=2.36=hf3e587d_33
  - bioconductor-qvalue=2.18.0=r36_1
  - blast=2.14.0=h7d5a4b4_1
  - bowtie2=2.5.1=py36hb79b6da_1
  - bwa=0.7.17=he4a0461_11
  - bwidget=1.9.14=ha770c72_1
  - bzip2=1.0.8=h7f98852_4
  - ca-certificates=2023.5.7=hbcca054_0
  - cairo=1.16.0=h18b612c_1001
  - centrifuge=1.0.4_beta=py36pl526he941832_2
  - curl=7.68.0=hf8cf82a_0
  - diamond=2.1.7=h5b5514e_0
  - entrez-direct=16.2=he881be0_1
  - expat=2.5.0=hcb278e6_1
  - fasttree=2.1.11=h031d066_2
  - fontconfig=2.14.2=h14ed4e7_0
  - freetype=2.12.1=hca18f0e_1
  - gcc_impl_linux-64=7.5.0=habd7529_20
  - gcc_linux-64=7.5.0=h47867f9_33
  - gettext=0.21.1=h27087fc_0
  - gfortran_impl_linux-64=7.5.0=h56cb351_20
  - gfortran_linux-64=7.5.0=h78c8a43_33
  - glib=2.66.3=h58526e2_0
  - graphite2=1.3.13=h58526e2_1001
  - gsl=2.5=h294904e_1
  - gxx_impl_linux-64=7.5.0=hd0bb8aa_20
  - gxx_linux-64=7.5.0=h555fc39_33
  - harfbuzz=2.4.0=h37c48d4_1
  - hmmer=3.3.2=hdbdd923_4
  - htslib=1.9=h244ad75_9
  - icu=58.2=hf484d3e_1000
  - infernal=1.1.4=h779adbc_0
  - iqtree=2.2.2.3=h2202e69_2
  - jpeg=9e=h0b41bf4_3
  - kernel-headers_linux-64=3.10.0=h4a8ded7_13
  - krb5=1.16.4=h2fd8d38_0
  - ld_impl_linux-64=2.36.1=hea4e1c9_2
  - lerc=4.0.0=h27087fc_0
  - libblas=3.9.0=13_linux64_openblas
  - libcblas=3.9.0=13_linux64_openblas
  - libcurl=7.68.0=hda55be3_0
  - libdeflate=1.14=h166bdaf_0
  - libedit=3.1.20191231=h46ee950_2
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.2.1=he1b5a44_1007
  - libgcc-devel_linux-64=7.5.0=hda03d7c_20
  - libgcc-ng=13.1.0=he5830b7_0
  - libgfortran-ng=7.5.0=h14aa051_20
  - libgfortran4=7.5.0=h14aa051_20
  - libglib=2.66.3=hbe7bbb4_0
  - libgomp=13.1.0=he5830b7_0
  - libhwloc=2.9.1=hd6dc26d_0
  - libiconv=1.17=h166bdaf_0
  - libidn2=2.3.4=h166bdaf_0
  - liblapack=3.9.0=13_linux64_openblas
  - libnsl=2.0.0=h7f98852_0
  - libopenblas=0.3.18=hf726d26_0
  - libpng=1.6.39=h753d276_0
  - libsqlite=3.42.0=h2797004_0
  - libssh2=1.10.0=haa6b8db_3
  - libstdcxx-devel_linux-64=7.5.0=hb016644_20
  - libstdcxx-ng=13.1.0=hfd8a6a1_0
  - libtiff=4.4.0=h82bc61c_5
  - libunistring=0.9.10=h7f98852_0
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp-base=1.3.0=h0b41bf4_0
  - libxcb=1.15=h0b41bf4_0
  - libxml2=2.10.3=hcbfbd50_0
  - libzlib=1.2.13=h166bdaf_4
  - llvm-openmp=8.0.1=hc9558a2_0
  - make=4.3=hd18ef5c_1
  - mcl=14.137=pl5262h779adbc_6
  - megahit=1.2.9=h43eeafb_4
  - muscle=3.8.1551=h7d875b9_6
  - ncurses=6.1=hf484d3e_1002
  - openmp=8.0.1=0
  - openssl=1.1.1u=hd590300_0
  - pandoc=2.19.2=h32600fe_2
  - pango=1.40.14=he7ab937_1005
  - pcre=8.45=h9c3ff4c_0
  - perl=5.26.2=h36c2ea0_1008
  - perl-archive-tar=2.32=pl526_0
  - perl-carp=1.38=pl526_3
  - perl-common-sense=3.74=pl526_2
  - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
  - perl-compress-raw-zlib=2.087=pl526hc9558a2_0
  - perl-exporter=5.72=pl526_1
  - perl-exporter-tiny=1.002001=pl526_0
  - perl-extutils-makemaker=7.36=pl526_1
  - perl-io-compress=2.087=pl526he1b5a44_0
  - perl-io-zlib=1.10=pl526_2
  - perl-json=4.02=pl526_0
  - perl-json-xs=2.34=pl526h6bb024c_3
  - perl-list-moreutils=0.428=pl526_1
  - perl-list-moreutils-xs=0.428=pl526_0
  - perl-pathtools=3.75=pl526h14c3975_1
  - perl-scalar-list-utils=1.52=pl526h516909a_0
  - perl-types-serialiser=1.0=pl526_2
  - perl-xsloader=0.24=pl526_0
  - pip=21.3.1=pyhd8ed1ab_0
  - pixman=0.38.0=h516909a_1003
  - prodigal=2.6.3=h031d066_6
  - pthread-stubs=0.4=h36c2ea0_1001
  - python=3.6.10=h8356626_1011_cpython
  - python_abi=3.6=2_cp36m
  - r-askpass=1.1=r36hcfec24a_2
  - r-assertthat=0.2.1=r36h6115d3f_2
  - r-backports=1.2.1=r36hcfec24a_0
  - r-base=3.6.1=h8900bf8_2
  - r-base64enc=0.1_3=r36hcfec24a_1004
  - r-blob=1.2.1=r36h6115d3f_1
  - r-brio=1.1.2=r36hcfec24a_0
  - r-broom=0.7.6=r36hc72bb7e_0
  - r-callr=3.7.0=r36hc72bb7e_0
  - r-cellranger=1.1.0=r36h6115d3f_1003
  - r-cli=2.5.0=r36hc72bb7e_0
  - r-clipr=0.7.1=r36h142f84f_0
  - r-colorspace=2.0_1=r36hcfec24a_0
  - r-cpp11=0.2.7=r36hc72bb7e_0
  - r-crayon=1.4.1=r36hc72bb7e_0
  - r-curl=4.3.1=r36hcfec24a_0
  - r-data.table=1.14.0=r36hcfec24a_0
  - r-dbi=1.1.1=r36hc72bb7e_0
  - r-dbplyr=2.1.1=r36hc72bb7e_0
  - r-desc=1.3.0=r36hc72bb7e_0
  - r-diffobj=0.3.4=r36hcfec24a_0
  - r-digest=0.6.27=r36h03ef668_0
  - r-dplyr=1.0.6=r36h03ef668_1
  - r-dtplyr=1.1.0=r36hc72bb7e_0
  - r-ellipsis=0.3.2=r36hcfec24a_0
  - r-evaluate=0.14=r36h6115d3f_2
  - r-fansi=0.4.2=r36hcfec24a_0
  - r-farver=2.1.0=r36h03ef668_0
  - r-forcats=0.5.1=r36hc72bb7e_0
  - r-fs=1.5.0=r36h0357c0b_0
  - r-gargle=1.1.0=r36hc72bb7e_0
  - r-generics=0.1.0=r36hc72bb7e_0
  - r-getopt=1.20.3=r36_2
  - r-ggplot2=3.3.3=r36hc72bb7e_0
  - r-glue=1.4.2=r36hcfec24a_0
  - r-googledrive=1.0.1=r36h6115d3f_1
  - r-googlesheets4=0.3.0=r36hc72bb7e_0
  - r-gtable=0.3.0=r36h6115d3f_3
  - r-haven=2.4.1=r36h2713e49_0
  - r-highr=0.9=r36hc72bb7e_0
  - r-hms=1.1.0=r36hc72bb7e_0
  - r-htmltools=0.5.1.1=r36h03ef668_0
  - r-httr=1.4.2=r36h6115d3f_0
  - r-ids=1.0.1=r36h6115d3f_1
  - r-isoband=0.2.4=r36h03ef668_0
  - r-jsonlite=1.7.2=r36hcfec24a_0
  - r-knitr=1.33=r36hc72bb7e_0
  - r-labeling=0.4.2=r36h142f84f_0
  - r-lattice=0.20_44=r36hcfec24a_0
  - r-lifecycle=1.0.0=r36hc72bb7e_0
  - r-lubridate=1.7.10=r36h03ef668_0
  - r-magrittr=2.0.1=r36hcfec24a_1
  - r-markdown=1.1=r36hcfec24a_1
  - r-mass=7.3_54=r36hcfec24a_0
  - r-matrix=1.3_3=r36he454529_0
  - r-mgcv=1.8_35=r36he454529_0
  - r-mime=0.10=r36hcfec24a_0
  - r-modelr=0.1.8=r36h6115d3f_0
  - r-munsell=0.5.0=r36h6115d3f_1003
  - r-nlme=3.1_150=r36h31ca83e_0
  - r-openssl=1.4.4=r36he36bf35_0
  - r-optparse=1.6.6=r36h6115d3f_1
  - r-pillar=1.6.1=r36hc72bb7e_0
  - r-pkgconfig=2.0.3=r36h6115d3f_1
  - r-pkgload=1.2.1=r36h03ef668_0
  - r-plyr=1.8.6=r36h0357c0b_1
  - r-praise=1.0.0=r36h6115d3f_1004
  - r-prettyunits=1.1.1=r36h6115d3f_1
  - r-processx=3.5.2=r36hcfec24a_0
  - r-progress=1.2.2=r36h6115d3f_2
  - r-ps=1.6.0=r36hcfec24a_0
  - r-purrr=0.3.4=r36hcfec24a_1
  - r-r6=2.5.0=r36hc72bb7e_0
  - r-rappdirs=0.3.3=r36hcfec24a_0
  - r-rcolorbrewer=1.1_2=r36h6115d3f_1003
  - r-rcpp=1.0.6=r36h03ef668_0
  - r-readr=1.4.0=r36h1b71b39_0
  - r-readxl=1.3.1=r36hde08347_4
  - r-rematch=1.0.1=r36h6115d3f_1003
  - r-rematch2=2.1.2=r36h6115d3f_1
  - r-reprex=2.0.0=r36hc72bb7e_0
  - r-reshape2=1.4.4=r36h0357c0b_1
  - r-rlang=0.4.11=r36hcfec24a_0
  - r-rmarkdown=2.8=r36hc72bb7e_0
  - r-rprojroot=2.0.2=r36hc72bb7e_0
  - r-rstudioapi=0.13=r36hc72bb7e_0
  - r-rvest=1.0.0=r36hc72bb7e_0
  - r-scales=1.1.1=r36h6115d3f_0
  - r-selectr=0.4_2=r36h6115d3f_1
  - r-stringi=1.4.3=r36h0357c0b_2
  - r-stringr=1.4.0=r36h6115d3f_2
  - r-sys=3.4=r36hcfec24a_0
  - r-testthat=3.0.2=r36h03ef668_0
  - r-tibble=3.1.2=r36hcfec24a_0
  - r-tidyr=1.1.3=r36h03ef668_0
  - r-tidyselect=1.1.1=r36hc72bb7e_0
  - r-tidyverse=1.3.1=r36hc72bb7e_0
  - r-tinytex=0.31=r36hc72bb7e_0
  - r-utf8=1.2.1=r36hcfec24a_0
  - r-uuid=0.1_4=r36hcdcec82_1
  - r-vctrs=0.3.8=r36hcfec24a_1
  - r-viridislite=0.4.0=r36hc72bb7e_0
  - r-waldo=0.2.5=r36hc72bb7e_0
  - r-withr=2.4.2=r36hc72bb7e_0
  - r-xfun=0.23=r36hcfec24a_0
  - r-xml2=1.3.2=r36h0357c0b_1
  - r-yaml=2.2.1=r36hcfec24a_1
  - readline=8.0=h46ee950_1
  - samtools=1.9=h10a08f8_12
  - sed=4.8=he412f7d_0
  - setuptools=58.0.4=py36h5fab9bb_2
  - spades=3.15.5=h95f258a_1
  - sqlite=3.32.3=hcee41ef_1
  - sysroot_linux-64=2.17=h4a8ded7_13
  - tbb=2021.9.0=hf52228f_0
  - tk=8.6.12=h27826a3_0
  - tktable=2.10=hb7b940f_3
  - trimal=1.4.1=h4ac6f70_8
  - trnascan-se=2.0.9=pl5262h779adbc_1
  - vmatch=2.3.0=hec16e2b_5
  - wget=1.20.3=ha56f1ee_1
  - wheel=0.37.1=pyhd8ed1ab_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.1.1=hd590300_0
  - xorg-libsm=1.2.4=h7391055_0
  - xorg-libx11=1.8.4=h8ee46fc_1
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.10=h5eee18b_1
  - zlib=1.2.13=h166bdaf_4
  - zstd=1.5.2=h3eb15da_6

mamba env create -n anvio_env -f anvio-dependencies.yml

curl -L https://github.com/merenlab/anvio/releases/download/v7.1/anvio-7.1.tar.gz > --output anvio-7.1.tar.gz
pip install anvio-7.1.tar.gz

meren commented 1 year ago

We tried this solution before, @jolespin. Environment YAML files are not a consistently good option for installation as a lot of people with different operating systems or even different versions of the same operating system run into problems quickly :(

jolespin commented 1 year ago

Oh bummer. Yea conda is kind of a black box sometimes. I've had the issues happen a couple of times installing QIIME2 but on one of the forums I was advised to run conda clean and it actually did solve the issue. I'm sure there's lots of edge cases.

meren commented 1 year ago

Mamba is faster than the YAML option. Setting up the environment literally takes a minute or two on a laptop since it installs all packages in parallel. Sorry mamba is broken on your system and good luck with the rest of your work :)

jolespin commented 1 year ago

Luckily it's only mamba init/activate that doesn't work but all other mamba processes like create, install and uninstall work perfectly. Major increase in speed.

alephreish commented 1 year ago

I wanted to add two more cents on the subject: conda is very popular and mamba is lightning fast at resolving environments. So, after playing a bit with the versions, I came up with the following environment definition that appears to pass anvi-self-test from bioconda::anvio=7:

channels:
 - conda-forge
 - bioconda
dependencies:
 - anvio=7
 - backports.zoneinfo=0.2.1
 - contextvars=2.4
 - asgiref=3.4.0
 - django=3.2.20
 - mistune=0.8.4
 - pip
 - pip:
   - scikit-learn==0.24.0

mamba env create -p anvio_env -f anvio.yaml

Resolving the environment takes ~25 sec. scikit-learn is updated from 0.20.3 to 0.24.0 with pipy.

The resulting environment looks as follows

````bash # packages in environment at anvio_env: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge _sysroot_linux-64_curr_repodata_hack 3 h69a702a_13 conda-forge alsa-lib 1.2.7.2 h166bdaf_0 conda-forge anvio 7 hdfd78af_1 bioconda anvio-minimal 7 py_0 bioconda appdirs 1.4.4 pyh9f0ad1d_0 conda-forge asgiref 3.4.0 pyhd8ed1ab_0 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.zoneinfo 0.2.1 py36h8f6f2f9_4 conda-forge binutils_impl_linux-64 2.39 he00db2b_1 conda-forge binutils_linux-64 2.39 h5fc0e48_13 conda-forge bioconductor-qvalue 2.26.0 r41hdfd78af_0 bioconda biopython 1.79 py36h8f6f2f9_0 conda-forge blast 2.5.0 hc0b0e79_3 bioconda blast-legacy 2.2.26 h9ee0642_3 bioconda boost 1.74.0 py36h355b2fd_3 conda-forge boost-cpp 1.74.0 h6cacc03_7 conda-forge bottle 0.12.23 pyhd8ed1ab_0 conda-forge bowtie2 2.4.5 py36hfca12d5_3 bioconda brotlipy 0.7.0 py36h8f6f2f9_1001 conda-forge bwa 0.7.17 he4a0461_11 bioconda bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cairo 1.16.0 ha12eb4b_1010 conda-forge centrifuge 1.0.3 py36pl5.22.0_1 bioconda certifi 2021.5.30 py36h5fab9bb_0 conda-forge cffi 1.14.6 py36hd8eec40_1 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge colored 1.4.4 pyhd8ed1ab_0 conda-forge configargparse 1.7 pyhd8ed1ab_0 conda-forge contextvars 2.4 py_0 conda-forge cryptography 35.0.0 py36hb60f036_0 conda-forge curl 7.86.0 h7bff187_1 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge datrie 0.8.2 py36h8f6f2f9_2 conda-forge dbus 1.13.6 h5008d03_3 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge diamond 2.1.8 h43eeafb_0 bioconda django 3.2.20 pyhd8ed1ab_0 conda-forge docutils 0.17.1 py36h5fab9bb_0 conda-forge ete3 3.1.2 pyh9f0ad1d_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fastani 1.34 h4dfc31f_0 bioconda fasttree 2.1.11 h031d066_2 bioconda font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gcc_impl_linux-64 10.4.0 h5231bdf_19 conda-forge gcc_linux-64 10.4.0 h9215b83_13 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran_impl_linux-64 10.4.0 h7d168d2_19 conda-forge gfortran_linux-64 10.4.0 h69d5af5_13 conda-forge gitdb 4.0.10 pyhd8ed1ab_0 conda-forge gitpython 3.1.18 pyhd8ed1ab_0 conda-forge glib 2.74.1 h6239696_0 conda-forge glib-tools 2.74.1 h6239696_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gsl 2.7 he838d99_0 conda-forge gst-plugins-base 1.20.3 h57caac4_2 conda-forge gstreamer 1.20.3 hd4edc92_2 conda-forge gxx_impl_linux-64 10.4.0 h5231bdf_19 conda-forge gxx_linux-64 10.4.0 h6e491c6_13 conda-forge harfbuzz 4.2.0 h40b6f09_0 conda-forge hmmer 3.3.2 hdbdd923_4 bioconda htslib 1.15.1 h9753748_0 bioconda icu 69.1 h9c3ff4c_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge illumina-utils 2.12 pyhdfd78af_0 bioconda immutables 0.16 py36h8f6f2f9_0 conda-forge importlib-metadata 4.8.1 py36h5fab9bb_0 conda-forge importlib_resources 5.4.0 pyhd8ed1ab_0 conda-forge infernal 1.1.2 h516909a_3 bioconda ipython_genutils 0.2.0 py_1 conda-forge iqtree 2.2.5 h21ec9f0_0 bioconda joblib 1.1.1 pypi_0 pypi jpeg 9e h0b41bf4_3 conda-forge jsonschema 4.1.2 pyhd8ed1ab_0 conda-forge jupyter_core 4.8.1 py36h5fab9bb_0 conda-forge kernel-headers_linux-64 3.10.0 h4a8ded7_13 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.3.1 py36h605e78d_1 conda-forge krb5 1.19.3 h3790be6_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge lerc 3.0 h9c3ff4c_0 conda-forge libblas 3.9.0 18_linux64_openblas conda-forge libcblas 3.9.0 18_linux64_openblas conda-forge libclang 13.0.1 default_h7634d5b_3 conda-forge libcurl 7.86.0 h7bff187_1 conda-forge libdeflate 1.10 h7f98852_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 h9b69904_4 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-devel_linux-64 10.4.0 hd38fd1e_19 conda-forge libgcc-ng 13.2.0 h807b86a_2 conda-forge libgfortran-ng 13.2.0 h69a702a_2 conda-forge libgfortran5 13.2.0 ha4646dd_2 conda-forge libglib 2.74.1 h7a41b64_0 conda-forge libgomp 13.2.0 h807b86a_2 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 18_linux64_openblas conda-forge libllvm10 10.0.1 he513fc3_3 conda-forge libllvm13 13.0.1 hf817b99_2 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 14.5 h72a31a5_3 conda-forge libsanitizer 10.4.0 h5246dfb_19 conda-forge libsqlite 3.43.0 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-devel_linux-64 10.4.0 hd38fd1e_19 conda-forge libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge libtiff 4.3.0 h0fcbabc_4 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.14 haae042b_4 conda-forge libxslt 1.1.33 h0ef7038_3 conda-forge libzlib 1.2.13 hd590300_5 conda-forge llvm-openmp 8.0.1 hc9558a2_0 conda-forge llvmlite 0.36.0 py36h05121d2_0 conda-forge lxml 4.6.3 py36h04a5ba7_0 conda-forge make 4.3 hd18ef5c_1 conda-forge matplotlib-base 3.3.4 py36hd391965_0 conda-forge mcl 14.137 h470a237_3 bioconda megahit 1.2.9 h43eeafb_4 bioconda mistune 0.8.4 pyh1a96a4e_1006 conda-forge mummer 3.23 pl5.22.0_5 bioconda muscle 5.1 h4ac6f70_3 bioconda mysql-common 8.0.32 h14678bc_0 conda-forge mysql-libs 8.0.32 h54cf53e_0 conda-forge nbformat 5.1.3 pyhd8ed1ab_0 conda-forge ncurses 6.4 hcb278e6_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.92 h1d7d5a4_0 conda-forge numba 0.53.1 py36h1328434_1 conda-forge numpy 1.19.5 py36hfc0c790_2 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjpeg 2.5.0 h7d73246_0 conda-forge openmp 8.0.1 0 conda-forge openssl 1.1.1w hd590300_0 conda-forge pandas 0.25.1 py36hb3f55d8_0 conda-forge pandoc 2.19.2 h32600fe_2 conda-forge pango 1.50.7 hbd2fdc8_0 conda-forge paste 3.5.3 pyhd8ed1ab_0 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre2 10.37 hc3806b6_1 conda-forge perl 5.22.0.1 0 conda-forge pillow 8.3.2 py36h676a545_0 conda-forge pip 21.3.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge prodigal 2.6.3 h031d066_6 bioconda psutil 5.4.3 py36_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyani 0.2.10 py_0 bioconda pycparser 2.21 pyhd8ed1ab_0 conda-forge pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pyqt 5.12.3 py36h5fab9bb_7 conda-forge pyqt-impl 5.12.3 py36h7ec31b9_7 conda-forge pyqt5-sip 4.19.18 py36hc4f0c31_7 conda-forge pyqtchart 5.12 py36h7ec31b9_7 conda-forge pyqtwebengine 5.12.1 py36h7ec31b9_7 conda-forge pyrsistent 0.17.3 py36h8f6f2f9_2 conda-forge pysam 0.19.1 py36hea1697a_0 bioconda pysocks 1.7.1 py36h5fab9bb_3 conda-forge python 3.6.15 hb7a2778_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-levenshtein 0.12.2 py36h8f6f2f9_0 conda-forge python_abi 3.6 2_cp36m conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py36h8f6f2f9_1 conda-forge qt 5.12.9 h1304e3e_6 conda-forge r-askpass 1.1 r41h06615bd_3 conda-forge r-assertthat 0.2.1 r41hc72bb7e_3 conda-forge r-backports 1.4.1 r41h06615bd_1 conda-forge r-base 4.1.3 hd930d0e_0 conda-forge r-base64enc 0.1_3 r41h06615bd_1005 conda-forge r-bit 4.0.5 r41h06615bd_0 conda-forge r-bit64 4.0.5 r41h06615bd_1 conda-forge r-blob 1.2.4 r41hc72bb7e_0 conda-forge r-broom 1.0.5 r41hc72bb7e_0 conda-forge r-bslib 0.5.0 r41hc72bb7e_0 conda-forge r-cachem 1.0.8 r41h57805ef_0 conda-forge r-callr 3.7.3 r41hc72bb7e_0 conda-forge r-cellranger 1.1.0 r41hc72bb7e_1005 conda-forge r-cli 3.6.1 r41h38f115c_0 conda-forge r-clipr 0.8.0 r41hc72bb7e_1 conda-forge r-colorspace 2.1_0 r41h133d619_0 conda-forge r-cpp11 0.4.3 r41hc72bb7e_0 conda-forge r-crayon 1.5.2 r41hc72bb7e_1 conda-forge r-curl 4.3.3 r41h06615bd_1 conda-forge r-data.table 1.14.8 r41h133d619_0 conda-forge r-dbi 1.1.3 r41hc72bb7e_1 conda-forge r-dbplyr 2.3.2 r41hc72bb7e_0 conda-forge r-digest 0.6.31 r41h38f115c_0 conda-forge r-dplyr 1.1.2 r41ha503ecb_0 conda-forge r-dtplyr 1.3.1 r41hc72bb7e_0 conda-forge r-ellipsis 0.3.2 r41h06615bd_1 conda-forge r-evaluate 0.21 r41hc72bb7e_0 conda-forge r-fansi 1.0.4 r41h133d619_0 conda-forge r-farver 2.1.1 r41h7525677_1 conda-forge r-fastmap 1.1.1 r41h38f115c_0 conda-forge r-fontawesome 0.5.1 r41hc72bb7e_0 conda-forge r-forcats 1.0.0 r41hc72bb7e_0 conda-forge r-fs 1.6.2 r41ha503ecb_0 conda-forge r-gargle 1.4.0 r41h785f33e_0 conda-forge r-generics 0.1.3 r41hc72bb7e_1 conda-forge r-getopt 1.20.3 r41ha770c72_3 conda-forge r-ggplot2 3.4.2 r41hc72bb7e_0 conda-forge r-glue 1.6.2 r41h06615bd_1 conda-forge r-googledrive 2.1.0 r41hc72bb7e_0 conda-forge r-googlesheets4 1.1.0 r41h785f33e_0 conda-forge r-gtable 0.3.3 r41hc72bb7e_0 conda-forge r-haven 2.5.2 r41h38f115c_0 conda-forge r-highr 0.10 r41hc72bb7e_0 conda-forge r-hms 1.1.3 r41hc72bb7e_0 conda-forge r-htmltools 0.5.5 r41h38f115c_0 conda-forge r-httr 1.4.6 r41hc72bb7e_0 conda-forge r-ids 1.0.1 r41hc72bb7e_2 conda-forge r-isoband 0.2.7 r41h38f115c_1 conda-forge r-jquerylib 0.1.4 r41hc72bb7e_1 conda-forge r-jsonlite 1.8.5 r41h57805ef_0 conda-forge r-knitr 1.43 r41hc72bb7e_0 conda-forge r-labeling 0.4.2 r41hc72bb7e_2 conda-forge r-lattice 0.21_8 r41h133d619_0 conda-forge 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merenlab / anvio