Conda is installing older version of Spades even though latest version is there in the bioconda repository

Question

[VenGeno]

I am trying to install spades using conda. Even though the bioconda has the latest version, the version getting installed in my system is an older version 3.13. Initially, I thought creating a new environment (with python 3.8) will resolve the issue. But still, conda is installing the old version. I am using conda version 23.1.0. I appreciate your help in this matter. Thank you in advance.

[josieclare]

Hi all, has anyone else faced the same problem as OP but not had a new environment solve the problem? I have been running into problems for every work around I can find, but cannot seem to be able to install a version of SPAdes above 3.13. And I need >= 3.14 to run Unicycler (which is ultimately my goal).

If I create a new environment again for this purpose, as above (using conda create -n spades -c bioconda spades=3.15.5), for example, I return the following error:

Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying 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 abort.
failed                                                                                                                

UnsatisfiableError:

Could it be to do with my linux kernel? Which is version 5.15.0

Any help very much appreciated!!

Answer 1

[ATpoint]

Try conda install -c bioconda spades=version, specifying the version you want.

[VenGeno]

I tried conda install -c bioconda spades=3.15.5 Yet the following happens and it now stays at

Retrieving notices: ...working... done 
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.

Then it stays like that.. Please see the conda info output for my base environment;

active environment: base
    active env location : /tmp/yes
            shell level : 1
       user config file : /home/ubuntu/.condarc
 populated config files : /home/ubuntu/.condarc
          conda version : 23.1.0
    conda-build version : 3.23.3
         python version : 3.9.16.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
 base environment : /tmp/yes  (writable)
      conda av data dir : /tmp/yes/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /tmp/yes/pkgs
                          /home/ubuntu/.conda/pkgs
       envs directories : /tmp/yes/envs
                          /home/ubuntu/.conda/envs
               platform : linux-64
             user-agent : conda/23.1.0 requests/2.28.1 CPython/3.9.16 Linux/5.15.0-1027-oracle ubuntu/22.04.1 glibc/2.35
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False

[cfos4698]

There might be dependency conflicts in your base environment. Try creating an environment containing the spades version you want (and whatever other tools you want in there).

conda create -n spades -c bioconda  spades=3.15.5

Also, I recommend using mamba to replace conda (https://github.com/mamba-org/mamba).

[VenGeno]

Thank You, cfos4698! It worked. Thank you for suggesting mamba. I will try it. Have a great day!

[ATpoint]

Indeed, a new environment is always recommended to keep things clean. +1 for mamba, it's just sooo! much faster.