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naumenko-sa avatar naumenko-sa commented on August 17, 2024

In the bcbio installation you may see:
/n/app/bcbio/1.2.9/anaconda/.condarc which sets the priority of the channels:

channels:
  - conda-forge
  - bioconda
  - defaults

So the higher priority are conda-forge and bioconda, but still some packages are installed from defaults channel,
you may see which by listing the packages in the env:

conda  list -p /n/app/bcbio/1.2.9/anaconda | grep -v conda-forge | grep -v bioconda
# packages in environment at /n/app/bcbio/1.2.9/anaconda:
#
# Name                    Version                   Build  Channel
bcbio-nextgen             1.2.9                    pypi_0    pypi
binutils_impl_linux-64    2.35.1               h27ae35d_9  
brotlipy                  0.7.0           py37h27cfd23_1003  
cffi                      1.14.6           py37h400218f_0  
chardet                   4.0.0           py37h06a4308_1003  
conda-package-handling    1.7.3            py37h27cfd23_1  
cryptography              3.4.7            py37hd23ed53_0  
curl                      7.80.0               h7f8727e_0  
gcc_impl_linux-64         9.3.0               h6df7d76_17  
gxx_impl_linux-64         9.3.0               hbdd7822_17  
idna                      2.10               pyhd3eb1b0_0  
ipython_genutils          0.2.0                    py37_0  
ld_impl_linux-64          2.35.1               h7274673_9  
libcurl                   7.80.0               h0b77cf5_0  
libffi                    3.3                  he6710b0_2  
libgcc-devel_linux-64     9.3.0               hb95220a_17  
libnghttp2                1.46.0               hce63b2e_0  
libstdcxx-devel_linux-64  9.3.0               hf0c5c8d_17  
ncurses                   6.2                  he6710b0_1  
pip                       21.1.3           py37h06a4308_0  
pycosat                   0.6.3            py37h27cfd23_0  
pycparser                 2.20                       py_2  
pyopenssl                 20.0.1             pyhd3eb1b0_1  
pysocks                   1.7.1                    py37_1  
python                    3.7.10               h12debd9_4  
readline                  8.1                  h27cfd23_0  
requests                  2.25.1             pyhd3eb1b0_0  
ruamel_yaml               0.15.100         py37h27cfd23_0  
setuptools                52.0.0           py37h06a4308_0  
six                       1.16.0             pyhd3eb1b0_0  
sqlite                    3.36.0               hc218d9a_0  
tk                        8.6.10               hbc83047_0  
tqdm                      4.61.2             pyhd3eb1b0_1  
urllib3                   1.26.6             pyhd3eb1b0_1  
wheel                     0.36.2             pyhd3eb1b0_0  
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
zstd                      1.5.0                ha4553b6_1  

see also:
https://docs.anaconda.com/free/anaconda/reference/default-repositories/

from bcbio-nextgen.

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