Comments (1)
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.
Related Issues (20)
- Does bcbio support smooth restart when a job is stopped? HOT 2
- Can bcbio customize the user-defined GLIBC directory? HOT 7
- bcbio run not running samples in parallel HOT 2
- mm10 Genome Installation Error
- miRBase certificate error
- miRBase genomes URLs have changed
- miRBase download files are not compressed
- Files are no longer available on miRBase ftp site
- miRBase old versions are no longer available
- resources assignment when perform parallel jobs HOT 1
- vcfanno bug
- Error upgrading bcbio-nextgen to add the genome and an aligner
- ATAC-seq
- ATAC-seq pipeline: what exampley is ready.bam? HOT 1
- MultiQC error: cannot import name 'TypedDict' from 'typing' HOT 2
- KeyError: 'MB1' ' returned non-zero exit status 1. when running scRNA-seq analysis for indropv3 HOT 1
- Hisat 2 error HOT 1
- File "abundance.h5" missing from salmon sample directory
- Installation fails HOT 3
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