installation using conda fails with UnsatisfiableError

[nettanetta]

Describe the bug Hi, I was trying to download pysradb using conda and the download failed: I tried installing pysradb to a new python 3.10 environment as instructed in the readme: conda create -c bioconda -n pysradb PYTHON=3.10 pysradb

It was stuck for a while, but in the end I got the following error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abor/
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package python conflicts for:
pysradb -> python[version=‘>3|>=3|>=3.7|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
python=3.10
pysradb -> lxml[version=‘>=4.6.3’] -> python[version=’2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.11,<3.12.0a0|>=3.9,<3.10.0a0|>=3.7,<4.0|>=3.6,<4.0|>=3.6|>=2.7|>=3.5,<3.6.0a0|>=3.7.1,<3.8.0a0|>=3.8']The following specifications were found to be incompatible with your system:
 - feature:/linux-64::__glibc==2.28=0
 - feature:/linux-64::__unix==0=0
 - feature:|@/linux-64::__unix==0=0
 - pysradb -> click[version=‘>=7.0’] -> __unix
 - pysradb -> click[version=‘>=7.0’] -> __win
 - python=3.10 -> libgcc-ng[version=‘>=10.3.0’] -> __glibc[version=‘>=2.17’]
Your installed version is: 0
Note that strict channel priority may have removed packages required for satisfiability.

To Reproduce I used the command : conda create -c bioconda -n pysradb PYTHON=3.10 pysradb using:

• OS: NAME="Debian GNU/Linux", VERSION_ID="11"
• Python version: 3.10
• conda 23.3.1

Can you please help? thanks! Netta

[saketkc]

Can you set the channel priority as recommended by bioconda:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

and then try with mamba create -n pysradb PYTHON=3.10 pysradb. As an aside, a faster alternative to conda is to use mamba: https://mamba.readthedocs.io/en/latest/

[saketkc]

Closing as I haven't heard back.

[nettanetta]

mamba worked for me! thank you very much for your help Netta