How to download DESeq2 in miniconda3 environment? - r

Question

I created an environment using miniconda3 with the following commands:
conda create -n r_ngs r-essentials r-base
source activate r_ngs
I needed to download some extra packages and I managed to download biomart and tximport with the following commands.
conda install -c bioconda bioconductor-tximport
conda install -c bioconda bioconductor-biomart
However, then I tried to install DESeq2 but I am getting errors. The command and errors are shown below.
conda install -c bioconda bioconductor-deseq2
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages. failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package libgcc-ng conflicts for:
bioconductor-deseq2 -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
bioconductor-deseq2 -> r-base[version='>=4.2,<4.3.0a0'] -> libgcc-ng[version='7.2.0.*|>=11.2.0|>=7.2.0']
Package libstdcxx-ng conflicts for:
bioconductor-deseq2 -> r-base[version='>=4.2,<4.3.0a0'] -> libstdcxx-ng[version='7.2.0.*|>=11.2.0|>=7.2.0']
bioconductor-deseq2 -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9']
Package xz conflicts for:
python=3.10 -> xz[version='>=5.2.5,<6.0a0|>=5.2.6,<6.0a0']
bioconductor-deseq2 -> r-base[version='>=4.2,<4.3.0a0'] -> xz[version='5.2.*|>=5.2.4,<6.0a0|>=5.2.5,<6.0a0']The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.35=0
- feature:|#/linux-64::__glibc==2.35=0
- python=3.10 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.35
The R version I have in the environment is R version 3.6.1 (2019-07-05).
How can I fix this?
Thank you

Answer 1

Bioconda has very specific channel requirements, namely:
conda-forge > bioconda > defaults
The best way to manage Conda environments is with YAMLs. One to use DESeq2 might look something like:
r_ngs.yaml
name: r_ngs
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- r-base=4.2
- bioconductor-deseq2
## additional packages...
and create it with
conda env create -n r_ngs -f r_ngs.yaml
Note, it is almost always preferable to declare all dependencies at time of creation of the environment.