cannot conda install macs3 on linux

Question

[QX]

Hi all,

I have tried to install MACS3 for peak calling from https://macs3-project.github.io/MACS/docs/INSTALL.html I have install all the required dependencies; however, when I install the MACS3, I running into error:

>     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.
>     This can take several minutes.  Press CTRL-C to abort.
>     failed                                                                                                                                                           
>     
>     UnsatisfiableError: The following specifications were found
>     to be incompatible with the existing python installation in your environment:
>     
>     Specifications:
>     
>       - macs3 -> python[version='>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.12,<3.13.0a0']
>     
>     Your python: python=3.11
>     
>     If python is on the left-most side of the chain, that's the version you've asked for.
>     When python appears to the right, that indicates that the thing on the left is somehow
>     not available for the python version you are constrained to. Note that conda will not
>     change your python version to a different minor version unless you explicitly specify
>     that.
>     
>     The following specifications were found to be incompatible with your system:
>     
>       - feature:/linux-64::__glibc==2.28=0
>       - python=3.11 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
>     
>     Your installed version is: 2.28
>     
>     Note that strict channel priority may have removed packages required for satisfiability.

Does anyone know which part I need to change to run the program?

Best,

Answer 1

[ATpoint]

I suggest you use the mamba package manager. Mamba is (for the end user) conda, just better and faster.

For installation, see https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html

Once installed and set up, make a new environment for the installation and install macs3 into it. Tested on Ubuntu, works without problems:

mamba create -n macs3_env bioconda::macs3

The :: notation tells mamba (and conda) in which channel it should look for macs3 (here bioconda channel).

If using conda, be sure to make a fresh environment first, you might have conflicts in the existing environment. Don't ever get the habit of spamming everything into the base environment, it becomes an unsolvable mess after a while.

[QX]

Hi ATpoint thank for suggestion and advice, I will try!