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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
792 stars 214 forks source link

ete3 with python3.6 and conda #430

Open marieBvr opened 4 years ago

marieBvr commented 4 years ago

Dear developer I encountered a problem when I tried to use ete3 with python3.6 and conda. I installed ete3 thanks to conda, following your guidelines. Then I tried to import ete3 from python3.6 with:

#!/home/myhome/anaconda3/bin/python
from ete3 import PhyloTree, Tree, NodeStyle, TreeStyle, SeqGroup, SeqMotifFace

Running this file, I obtained these errors:

Traceback (most recent call last):
  File "/home/myhome/anaconda3/lib/python3.6/site-packages/ete3/treeview/faces.py", line 52, in <module>
    from urllib2 import urlopen
ModuleNotFoundError: No module named 'urllib2'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/myhome/script.py", line 5, in <module>
    from ete3 import PhyloTree, Tree, NodeStyle, TreeStyle, SeqGroup, SeqMotifFace
  File "/home/myhome/anaconda3/lib/python3.6/site-packages/ete3/__init__.py", line 52, in <module>
    from .coretype.tree import *
  File "/home/myhome/anaconda3/lib/python3.6/site-packages/ete3/coretype/tree.py", line 57, in <module>
    from ..treeview.main import NodeStyle, _FaceAreas, FaceContainer, FACE_POSITIONS
  File "/home/myhome/anaconda3/lib/python3.6/site-packages/ete3/treeview/__init__.py", line 43, in <module>
    from .faces import *
  File "/home/myhome/anaconda3/lib/python3.6/site-packages/ete3/treeview/faces.py", line 54, in <module>
    from urllib.request import urlopen
  File "/home/myhome/anaconda3/lib/python3.6/urllib/request.py", line 88, in <module>
    import http.client
  File "/home/myhome/anaconda3/lib/python3.6/http/client.py", line 71, in <module>
    import email.parser
  File "/home/myhome/anaconda3/lib/python3.6/email/parser.py", line 12, in <module>
    from email.feedparser import FeedParser, BytesFeedParser
  File "/home/myhome/anaconda3/lib/python3.6/email/feedparser.py", line 27, in <module>
    from email._policybase import compat32
  File "/home/myhome/anaconda3/lib/python3.6/email/_policybase.py", line 9, in <module>
    from email.utils import _has_surrogates
  File "/home/myhome/anaconda3/lib/python3.6/email/utils.py", line 29, in <module>
    import socket
  File "/home/myhome/anaconda3/lib/python3.6/socket.py", line 52, in <module>
    import os, sys, io, selectors
  File "/home/myhome/anaconda3/lib/python3.6/selectors.py", line 290, in <module>
    class SelectSelector(_BaseSelectorImpl):
  File "/home/myhome/anaconda3/lib/python3.6/selectors.py", line 317, in SelectSelector
    _select = select.select
AttributeError: module 'select' has no attribute 'select'

I solved these problem by: 1/ modifying ete3/treeview/faces.py changing from urllib2 import urlopen by from urllib3 import urlopen 2/ modifying anaconda3/lib/python3.6/selectors.py

    if sys.platform == 'win32':
        def _select(self, r, w, _, timeout=None):
            r, w, x = select.select(r, w, w, timeout)
            return r, w + x, []
    else:
        _select = select.select

by 

    if sys.platform == 'win32':
        def _select(self, r, w, _, timeout=None):
            r, w, x = select.select(r, w, w, timeout)
            return r, w + x, []
    else:
        _select = select

I think that not everything is due to the ete3 source code but I hope that my suggestions will help someone dealing with these issues.

Best, Marie

SilasK commented 3 years ago

I also get problems with python 3.6

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-6-a14301107248> in <module>
     21 
     22 
---> 23 ts=ete3.TreeStyle()
     24 ts.mode='c'
     25 ts.show_leaf_name=False

AttributeError: module 'ete3' has no attribute 'TreeStyle'

My conda env : python 3.6 and qt 5


# packages in environment at /srv/conda/envs/notebook:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
alembic                   1.4.2              pyh9f0ad1d_0    conda-forge
altair                    4.1.0                      py_1    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
bleach                    3.1.5              pyh9f0ad1d_0    conda-forge
blinker                   1.4                        py_1    conda-forge
brotlipy                  0.7.0           py36h8c4c3a4_1000    conda-forge
ca-certificates           2020.6.20            hecda079_0    conda-forge
cachecontrol              0.12.6                     py_0    conda-forge
certifi                   2020.6.20        py36h9f0ad1d_0    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.14.0           py36hd463f26_0    conda-forge
chardet                   3.0.4           py36h9f0ad1d_1006    conda-forge
cryptography              3.0              py36h45558ae_0    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
cython                    0.29.21          py36ha357f81_1    conda-forge
dbus                      1.13.6               hfdff14a_1    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             py36h9f0ad1d_1001    conda-forge
ete3                      3.1.2              pyh9f0ad1d_0    conda-forge
expat                     2.2.9                he1b5a44_2    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.4               he06d7ca_0    conda-forge
gettext                   0.19.8.1          hf34092f_1004    conda-forge
glib                      2.66.3               h58526e2_0    conda-forge
gst-plugins-base          1.14.5               h0935bb2_2    conda-forge
gstreamer                 1.14.5               h36ae1b5_2    conda-forge
hdmedians                 0.14.1           py36h68bb277_1    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
importlib-metadata        1.7.0            py36h9f0ad1d_0    conda-forge
importlib_metadata        1.7.0                         0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
ipykernel                 5.3.4            py36h95af2a2_0    conda-forge
ipython                   7.16.1           py36h95af2a2_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
jedi                      0.17.2           py36h9f0ad1d_0    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
joblib                    0.17.0                     py_0    conda-forge
jpeg                      9d                   h516909a_0    conda-forge
json5                     0.9.4              pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0            py36h9f0ad1d_1    conda-forge
jupyter-offlinenotebook   0.1.0                    pypi_0    pypi
jupyter_client            6.1.6                      py_0    conda-forge
jupyter_core              4.6.3            py36h9f0ad1d_1    conda-forge
jupyter_telemetry         0.0.5                      py_0    conda-forge
jupyterhub-base           1.1.0                    py36_2    conda-forge
jupyterhub-singleuser     1.1.0                    py36_2    conda-forge
jupyterlab                2.2.0                      py_0    conda-forge
jupyterlab_server         1.2.0                      py_0    conda-forge
kiwisolver                1.3.1            py36h51d7077_0    conda-forge
krb5                      1.17.1               hfafb76e_1    conda-forge
lcms2                     2.11                 hcbb858e_1    conda-forge
ld_impl_linux-64          2.34                 h53a641e_7    conda-forge
libblas                   3.9.0                3_openblas    conda-forge
libcblas                  3.9.0                3_openblas    conda-forge
libclang                  9.0.1           default_hde54327_0    conda-forge
libcurl                   7.71.1               hcdd3856_3    conda-forge
libedit                   3.1.20191231         h46ee950_1    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.5.0               hae1eefd_17    conda-forge
libgfortran4              7.5.0               hae1eefd_17    conda-forge
libglib                   2.66.3               hbe7bbb4_0    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                3_openblas    conda-forge
libllvm9                  9.0.1                he513fc3_1    conda-forge
libopenblas               0.3.12          pthreads_hb3c22a3_1    conda-forge
libpng                    1.6.37               hed695b0_2    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libssh2                   1.9.0                hab1572f_4    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc7e4089_6    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libwebp-base              1.1.0                h516909a_3    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxkbcommon              0.10.0               he1b5a44_0    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
libxslt                   1.1.33               h31b3aaa_0    conda-forge
lockfile                  0.12.2                   py36_0    conda-forge
lxml                      4.6.1            py36h17c4326_0    conda-forge
lz4-c                     1.9.2                he1b5a44_3    conda-forge
mako                      1.1.0                      py_0    conda-forge
markupsafe                1.1.1            py36h8c4c3a4_1    conda-forge
matplotlib                3.3.3            py36h5fab9bb_0    conda-forge
matplotlib-base           3.3.3            py36he12231b_0    conda-forge
mistune                   0.8.4           py36h8c4c3a4_1001    conda-forge
more-itertools            8.6.0              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.0            py36hdb11119_2    conda-forge
natsort                   7.1.0              pyhd8ed1ab_0    conda-forge
nbconvert                 5.6.1            py36h9f0ad1d_1    conda-forge
nbformat                  5.0.7                      py_0    conda-forge
nbgitpuller               0.9.0                      py_0    conda-forge
nbresuse                  0.3.3                      py_0    conda-forge
ncurses                   6.2                  he1b5a44_1    conda-forge
notebook                  6.0.3            py36h9f0ad1d_1    conda-forge
nspr                      4.29                 he1b5a44_1    conda-forge
nss                       3.55                 he751ad9_0    conda-forge
nteract_on_jupyter        2.1.3                      py_0    conda-forge
numpy                     1.19.4           py36h8732dcd_1    conda-forge
oauthlib                  3.0.1                      py_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openssl                   1.1.1g               h516909a_0    conda-forge
packaging                 20.4               pyh9f0ad1d_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    0.25.3           py36hb3f55d8_0    conda-forge
pandoc                    2.10.1               h516909a_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.7.1              pyh9f0ad1d_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.44                 he1b5a44_0    conda-forge
pexpect                   4.8.0            py36h9f0ad1d_1    conda-forge
pickleshare               0.7.5           py36h9f0ad1d_1001    conda-forge
pillow                    8.0.1            py36h8328e55_0    conda-forge
pip                       20.1.1                     py_1    conda-forge
pluggy                    0.13.1           py36h9880bd3_3    conda-forge
prometheus_client         0.8.0              pyh9f0ad1d_0    conda-forge
prompt-toolkit            3.0.5                      py_1    conda-forge
psutil                    5.7.2            py36h8c4c3a4_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
py                        1.9.0              pyh9f0ad1d_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pycurl                    7.43.0.5         py36h2e6c563_2    conda-forge
pygments                  2.6.1                      py_0    conda-forge
pyjwt                     1.7.1                      py_0    conda-forge
pyopenssl                 19.1.0                     py_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.12.3           py36haa643ae_3    conda-forge
pyqt5-sip                 4.19.18                  pypi_0    pypi
pyqtchart                 5.12                     pypi_0    pypi
pyqtwebengine             5.12.1                   pypi_0    pypi
pyrsistent                0.16.0           py36h8c4c3a4_0    conda-forge
pysocks                   1.7.1            py36h9f0ad1d_1    conda-forge
pytest                    6.1.2            py36h5fab9bb_0    conda-forge
python                    3.6.11          h425cb1d_0_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-json-logger        0.1.11                     py_0    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
pytz                      2020.4             pyhd8ed1ab_0    conda-forge
pyzmq                     19.0.1           py36h9947dbf_0    conda-forge
qt                        5.12.5               hd8c4c69_1    conda-forge
readline                  8.0                  he28a2e2_2    conda-forge
requests                  2.24.0             pyh9f0ad1d_0    conda-forge
ruamel.yaml               0.16.6           py36h8c4c3a4_1    conda-forge
ruamel.yaml.clib          0.2.0            py36h8c4c3a4_1    conda-forge
scikit-bio                0.5.5           py36h3010b51_1000    conda-forge
scikit-learn              0.23.2           py36hb6e6923_3    conda-forge
scipy                     1.5.3            py36h976291a_0    conda-forge
seaborn                   0.11.0               ha770c72_1    conda-forge
seaborn-base              0.11.0             pyhd8ed1ab_1    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.2.0           py36h9f0ad1d_0    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlalchemy                1.3.18           py36h8c4c3a4_0    conda-forge
sqlite                    3.32.3               hcee41ef_1    conda-forge
statsmodels               0.12.1           py36ha112f06_1    conda-forge
terminado                 0.8.3            py36h9f0ad1d_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
threadpoolctl             2.1.0              pyh5ca1d4c_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.11.1                     py_0    conda-forge
tornado                   6.0.4            py36h8c4c3a4_1    conda-forge
traitlets                 4.3.3            py36h9f0ad1d_1    conda-forge
urllib3                   1.25.10                    py_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.34.2                     py_1    conda-forge
widgetsnbextension        3.5.1            py36h9f0ad1d_1    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zipp                      3.1.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.5                h6597ccf_2    conda-forge
SilasK commented 3 years ago

With python 3.8 It works

# packages in environment at /Users/silas/miniconda3:
#
# Name                    Version                   Build  Channel
abseil-cpp                20200923.3           h046ec9c_0    conda-forge
aioeasywebdav             2.4.0           py38h50d1736_1001    conda-forge
aiohttp                   3.7.4            py38h96a0964_0    conda-forge
altair                    4.1.0                      py_1    conda-forge
amply                     0.1.4                      py_0    conda-forge
anyio                     2.2.0            py38h50d1736_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
appnope                   0.1.2            py38h50d1736_1    conda-forge
argon2-cffi               20.1.0           py38h5406a74_2    conda-forge
arrow-cpp                 3.0.0           py38h13a1b12_7_cpu    conda-forge
async-timeout             3.0.1                   py_1000    conda-forge
async_generator           1.10                       py_0    conda-forge
attmap                    0.12.11                    py_0    conda-forge
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
aws-c-cal                 0.4.5                h812e40e_7    conda-forge
aws-c-common              0.5.1                hbcf498f_0    conda-forge
aws-c-event-stream        0.2.7                h8f4fc19_0    conda-forge
aws-c-io                  0.9.0                haf44f29_1    conda-forge
aws-checksums             0.1.11               h6c46989_2    conda-forge
aws-sdk-cpp               1.8.138              h899596b_3    conda-forge
babel                     2.9.0              pyhd3deb0d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
bbmap                     38.90                hf29c6f4_0    bioconda
bcrypt                    3.2.0            py38h5406a74_1    conda-forge
blas                      1.0                         mkl  
bleach                    3.3.0              pyh44b312d_0    conda-forge
boto                      2.49.0                     py_0    conda-forge
boto3                     1.17.22            pyhd8ed1ab_0    conda-forge
botocore                  1.20.22            pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h046ec9c_4    conda-forge
brotlipy                  0.7.0           py38h9ed2024_1003  
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.8                hc929b4f_4    conda-forge
c-ares                    1.17.1               hc929b4f_0    conda-forge
ca-certificates           2021.1.19            hecd8cb5_1  
cachecontrol              0.12.6                     py_0    conda-forge
cachetools                4.2.1              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            ha8983da_1005    conda-forge
certifi                   2020.12.5        py38h50d1736_1    conda-forge
cffi                      1.14.3           py38h2125817_2  
chardet                   3.0.4           py38hecd8cb5_1003  
coincbc                   2.10.3               h7a5a08d_3    conda-forge
conda                     4.9.2            py38h50d1736_0    conda-forge
conda-package-handling    1.7.2            py38h22f3db7_0  
configargparse            1.3                pyhd8ed1ab_0    conda-forge
cryptography              3.2.1            py38hbcfaee0_1  
cycler                    0.10.0                     py_2    conda-forge
cython                    0.29.22          py38h91a8764_0    conda-forge
datrie                    0.8.2            py38h4d0b108_1    conda-forge
dbus                      1.13.18              h18a8e69_0  
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
docutils                  0.16             py38h50d1736_3    conda-forge
dropbox                   11.2.0             pyhd8ed1ab_0    conda-forge
entrypoints               0.3             py38h32f6830_1002    conda-forge
et_xmlfile                1.0.1                   py_1001    conda-forge
ete3                      3.1.2              pyh9f0ad1d_0    conda-forge
expat                     2.2.10               h1c7c35f_0    conda-forge
fastcluster               1.1.26           py38h6be0db6_2    conda-forge
fftw                      3.3.9                h9ed2024_1  
filechunkio               1.8                        py_2    conda-forge
filelock                  3.0.12             pyh9f0ad1d_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      2.001                hab24e00_0    conda-forge
font-ttf-source-code-pro  2.030                hab24e00_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hd23ceaa_1004    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
ftputil                   5.0.0              pyhd8ed1ab_0    conda-forge
gdk-pixbuf                2.38.2               h1464050_6    conda-forge
gettext                   0.19.8.1          h7937167_1005    conda-forge
gflags                    2.2.2             hb1e8313_1004    conda-forge
ghostscript               9.53.3               h2e338ed_2    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
gitdb                     4.0.5              pyhd8ed1ab_1    conda-forge
gitpython                 3.1.14             pyhd8ed1ab_0    conda-forge
glib                      2.67.4               hdf23fa2_1  
glog                      0.4.0                hb7f4fc5_3    conda-forge
gobject-introspection     1.66.1           py38hb1419e7_0  
google-api-core           1.25.1             pyhd8ed1ab_0    conda-forge
google-api-python-client  2.0.2              pyhd8ed1ab_0    conda-forge
google-auth               1.27.1             pyhd3eb1b0_0  
google-auth-httplib2      0.0.4              pyh9f0ad1d_0    conda-forge
google-cloud-core         1.6.0              pyhd3eb1b0_0  
google-cloud-storage      1.36.1             pyhd3eb1b0_0  
google-crc32c             1.1.2            py38haea9d43_0    conda-forge
google-resumable-media    1.2.0              pyhd3deb0d_0    conda-forge
googleapis-common-protos  1.52.0           py38h50d1736_1    conda-forge
graphite2                 1.3.14               h38d11af_0  
graphviz                  2.42.3               h98dfb87_0    conda-forge
grpc-cpp                  1.36.0               h7ffa9ba_0    conda-forge
harfbuzz                  2.7.2                h8810732_0    conda-forge
hdbscan                   0.8.27           py38ha1b04c9_0    conda-forge
hdmedians                 0.14.2           py38h8cc9b4f_0    conda-forge
httplib2                  0.19.0             pyhd8ed1ab_0    conda-forge
icu                       67.1                 hb1e8313_0    conda-forge
idna                      2.10                       py_0  
imagemagick               7.0.10_28       pl5262h9a5bc03_1    conda-forge
importlib-metadata        3.7.0            py38h50d1736_0    conda-forge
importlib_metadata        3.7.0                hd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
ipykernel                 5.5.0            py38h9bb44b7_1    conda-forge
ipython                   7.21.0           py38h9bb44b7_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jbig                      2.1               h0d85af4_2002    conda-forge
jdcal                     1.4.1                      py_0    conda-forge
jedi                      0.18.0           py38h50d1736_2    conda-forge
jinja2                    2.11.3             pyh44b312d_0    conda-forge
jmespath                  0.10.0             pyh9f0ad1d_0    conda-forge
joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   hbcb3906_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0            py38h32f6830_1    conda-forge
jupyter-packaging         0.7.12             pyhd8ed1ab_0    conda-forge
jupyter_client            6.1.11             pyhd8ed1ab_1    conda-forge
jupyter_core              4.7.1            py38h50d1736_0    conda-forge
jupyter_server            1.4.1            py38h50d1736_0    conda-forge
jupyterlab                3.0.9              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_server         2.3.0              pyhd8ed1ab_0    conda-forge
kiwisolver                1.3.1            py38hd9c93a9_1    conda-forge
krb5                      1.17.2               h60d9502_0    conda-forge
lcms2                     2.12                 h577c468_0    conda-forge
libarchive                3.5.1                h0a5793d_1    conda-forge
libblas                   3.8.0                    14_mkl    conda-forge
libcblas                  3.8.0                    14_mkl    conda-forge
libclang                  10.0.1          default_hf57f61e_1    conda-forge
libcrc32c                 1.1.1                hb1e8313_2    conda-forge
libcurl                   7.71.1               h9bf37e3_8    conda-forge
libcxx                    11.0.1               habf9029_0    conda-forge
libedit                   3.1.20191231         h1de35cc_1  
libev                     4.33                 haf1e3a3_1    conda-forge
libevent                  2.1.10               hddc9c9b_3    conda-forge
libffi                    3.3                  hb1e8313_2  
libgfortran               3.0.1                         0    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.8.0                    14_mkl    conda-forge
libllvm10                 10.0.1               h009f743_3    conda-forge
libllvm11                 11.0.1               h223d4b2_0    conda-forge
libnghttp2                1.43.0               h07e645a_0    conda-forge
libpng                    1.6.37               hb0a8c7a_2    conda-forge
libpq                     12.3                 h7049927_3    conda-forge
libprotobuf               3.15.3               hcf210ce_0    conda-forge
librsvg                   2.50.2               hefc9941_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsolv                   0.7.17               hfd3ada9_0    conda-forge
libssh2                   1.9.0                h8a08a2b_5    conda-forge
libthrift                 0.13.0               h8459986_6    conda-forge
libtiff                   4.2.0                h355d032_0    conda-forge
libutf8proc               2.6.1                h35c211d_0    conda-forge
libwebp                   1.2.0                h1648767_0    conda-forge
libwebp-base              1.2.0                hbcf498f_0    conda-forge
libxcb                    1.13              h35c211d_1003    conda-forge
libxml2                   2.9.10               h7fdee97_2    conda-forge
libxslt                   1.1.33               hfed2d9b_1    conda-forge
llvm-openmp               11.0.1               h7c73e74_0    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
logmuse                   0.2.6              pyh8c360ce_0    conda-forge
lxml                      4.6.2            py38h7d97eb6_1    conda-forge
lz4-c                     1.9.3                h046ec9c_0    conda-forge
lzo                       2.10              haf1e3a3_1000    conda-forge
mamba                     0.7.14           py38hb989c8f_0    conda-forge
markupsafe                1.1.1            py38h5406a74_3    conda-forge
matplotlib                3.3.4            py38h50d1736_0    conda-forge
matplotlib-base           3.3.4            py38hb24f337_0    conda-forge
matplotlib-venn           0.11.6             pyh9f0ad1d_0    conda-forge
mistune                   0.8.4           py38h5406a74_1003    conda-forge
mkl                       2019.5                      281    conda-forge
mkl-service               2.3.0            py38h0b31af3_0    conda-forge
more-itertools            8.7.0              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.2            py38hd9c93a9_1    conda-forge
multidict                 5.1.0            py38h5406a74_1    conda-forge
mysql-common              8.0.21                        2    conda-forge
mysql-libs                8.0.21               hfb8f7af_2    conda-forge
natsort                   7.1.1              pyhd8ed1ab_0    conda-forge
nbclassic                 0.2.6              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.3              pyhd8ed1ab_0    conda-forge
nbconvert                 6.0.7            py38h50d1736_3    conda-forge
nbformat                  5.1.2              pyhd8ed1ab_1    conda-forge
ncurses                   6.2                  h0a44026_1  
nest-asyncio              1.5.1              pyhd3eb1b0_0  
networkx                  2.5                        py_0    conda-forge
notebook                  6.2.0            py38h50d1736_0    conda-forge
nspr                      4.29                 hbc8d48c_1    conda-forge
nss                       3.47                 hcec2283_0    conda-forge
numpy                     1.20.1           py38h64deac9_0    conda-forge
oauth2client              4.1.3                      py_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjdk                   11.0.8               hb0a8c7a_0    conda-forge
openjpeg                  2.3.1                hcdae239_3    conda-forge
openpyxl                  3.0.6              pyhd8ed1ab_0    conda-forge
openssl                   1.1.1j               hbcf498f_0    conda-forge
orc                       1.6.7                hb8e0f11_1    conda-forge
packaging                 20.9               pyh44b312d_0    conda-forge
pandas                    1.2.2            py38hb77cc89_0    conda-forge
pandoc                    2.11.4               h35c211d_0    conda-forge
pandocfilters             1.4.3            py38hecd8cb5_1  
pango                     1.42.4               haa940fe_4    conda-forge
paramiko                  2.7.2              pyh9f0ad1d_0    conda-forge
parquet-cpp               1.5.1                         1    conda-forge
parso                     0.8.1              pyhd8ed1ab_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pbzip2                    1.1.13               h9d27c22_1    conda-forge
pcre                      8.44                 hb1e8313_0    conda-forge
peppy                     0.31.0             pyh9f0ad1d_0    conda-forge
perl                      5.26.2            hbcb3906_1008    conda-forge
pexpect                   4.8.0            py38h32f6830_1    conda-forge
pickleshare               0.7.5           py38h32f6830_1002    conda-forge
pillow                    8.1.1            py38h83525de_0    conda-forge
pip                       20.2.4           py38hecd8cb5_0  
pixman                    0.38.0            h01d97ff_1003    conda-forge
pkg-config                0.29.2            hb849cc2_1008    conda-forge
pluggy                    0.13.1           py38h50d1736_4    conda-forge
ply                       3.11                       py_1    conda-forge
prettytable               2.1.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.9.0              pyhd3deb0d_0    conda-forge
prompt-toolkit            3.0.16             pyha770c72_0    conda-forge
protobuf                  3.15.3           py38ha048514_0    conda-forge
psutil                    5.8.0            py38h5406a74_1    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulp                      2.4              py38h50d1736_0    conda-forge
py                        1.10.0             pyhd3deb0d_0    conda-forge
pyarrow                   3.0.0           py38h5def71b_7_cpu    conda-forge
pyasn1                    0.4.8                      py_0    conda-forge
pyasn1-modules            0.2.8                      py_0  
pycosat                   0.6.3            py38h1de35cc_1  
pycparser                 2.20                       py_2  
pygments                  2.8.0              pyhd8ed1ab_0    conda-forge
pygraphviz                1.7              py38hfe84aab_0    conda-forge
pynacl                    1.4.0            py38h5406a74_2    conda-forge
pyopenssl                 19.1.0             pyhd3eb1b0_1  
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyqt                      5.12.3           py38h50d1736_7    conda-forge
pyqt-impl                 5.12.3           py38h721a93c_7    conda-forge
pyqt5-sip                 4.19.18          py38h5745d40_7    conda-forge
pyqtchart                 5.12             py38h721a93c_7    conda-forge
pyqtwebengine             5.12.1           py38h721a93c_7    conda-forge
pyrsistent                0.17.3           py38h5406a74_2    conda-forge
pysftp                    0.2.9                      py_1    conda-forge
pysocks                   1.7.1                    py38_1  
pytest                    6.2.2            py38h50d1736_0    conda-forge
python                    3.8.5                h26836e1_1  
python-dateutil           2.8.1                      py_0    conda-forge
python-irodsclient        0.8.6              pyhd8ed1ab_0    conda-forge
python.app                2                       py38_10  
python_abi                3.8                      1_cp38    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
pyyaml                    5.4.1            py38h5406a74_0    conda-forge
pyzmq                     22.0.3           py38hd3b92b6_1    conda-forge
qt                        5.12.9               h717870c_0    conda-forge
ratelimiter               1.2.0           py38h32f6830_1001    conda-forge
re2                       2020.11.01           h2e338ed_0    conda-forge
readline                  8.0                  h1de35cc_0  
reproc                    14.2.1               hbcb3906_0    conda-forge
reproc-cpp                14.2.1               h2e338ed_0    conda-forge
requests                  2.24.0                     py_0  
rsa                       4.7.2              pyh44b312d_0    conda-forge
ruamel_yaml               0.15.87          py38haf1e3a3_1  
s3transfer                0.3.4              pyhd8ed1ab_0    conda-forge
scikit-bio                0.5.6            py38hf3d72b9_4    conda-forge
scikit-learn              0.24.1           py38hfd19401_0    conda-forge
scikit-learn-extra        0.1.0b2          py38h65ad66c_0    conda-forge
scipy                     1.6.1            py38h2515648_0  
seaborn                   0.11.1               h694c41f_0    conda-forge
seaborn-base              0.11.1             pyhd8ed1ab_1    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                50.3.1           py38hecd8cb5_1  
simplejson                3.17.2           py38h5406a74_2    conda-forge
six                       1.15.0           py38hecd8cb5_0  
slacker                   0.14.0                     py_0    conda-forge
smart_open                4.2.0              pyhd8ed1ab_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
snakemake                 6.0.2                         0    bioconda
snakemake-minimal         6.0.2                      py_0    bioconda
snappy                    1.1.8                hb1e8313_3    conda-forge
sniffio                   1.2.0            py38h50d1736_1    conda-forge
sqlite                    3.34.0               h17101e1_0    conda-forge
statsmodels               0.12.2           py38ha1b04c9_0    conda-forge
stone                     3.2.1              pyhd8ed1ab_0    conda-forge
svgutils                  0.3.1                   py_1000    conda-forge
terminado                 0.9.2            py38h50d1736_0    conda-forge
testpath                  0.4.4                      py_0    conda-forge
threadpoolctl             2.1.0              pyh5ca1d4c_0    conda-forge
tk                        8.6.10               hb0a8c7a_0  
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
toolz                     0.11.1                     py_0    conda-forge
toposort                  1.6                pyhd8ed1ab_0    conda-forge
tornado                   6.1              py38h5406a74_1    conda-forge
tqdm                      4.51.0             pyhd3eb1b0_0  
traitlets                 5.0.5                      py_0    conda-forge
typing-extensions         3.7.4.3                       0    conda-forge
typing_extensions         3.7.4.3                    py_0    conda-forge
ubiquerg                  0.6.1              pyh9f0ad1d_0    conda-forge
uritemplate               3.0.1                      py_0    conda-forge
urllib3                   1.25.11                    py_0  
veracitools               0.1.3                      py_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.35.1             pyhd3eb1b0_0  
wrapt                     1.12.1           py38h5406a74_3    conda-forge
xlrd                      2.0.1              pyhd8ed1ab_3    conda-forge
xmlrunner                 1.7.7                      py_0    conda-forge
xorg-kbproto              1.0.7             h35c211d_1002    conda-forge
xorg-libice               1.0.10               h01d97ff_0    conda-forge
xorg-libsm                1.2.3             h1de35cc_1000    conda-forge
xorg-libx11               1.6.12               haf1e3a3_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xorg-libxext              1.3.4                h01d97ff_0    conda-forge
xorg-libxrender           0.9.10            h1de35cc_1002    conda-forge
xorg-libxt                1.2.1                h35c211d_0    conda-forge
xorg-renderproto          0.11.1            h1de35cc_1002    conda-forge
xorg-xextproto            7.3.0             h35c211d_1002    conda-forge
xorg-xproto               7.0.31            h35c211d_1007    conda-forge
xz                        5.2.5                h1de35cc_0  
yaml                      0.2.5                haf1e3a3_0  
yarl                      1.5.1            py38h4d0b108_0    conda-forge
zeromq                    4.3.4                h1c7c35f_0    conda-forge
zipp                      3.4.0                      py_0    conda-forge
zlib                      1.2.11               h1de35cc_3  
zstd                      1.4.8                hf387650_1    conda-forge