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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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conda installed prokka not working due to too old conda install tbl2asn #488

Closed Casperjamin closed 4 years ago

Casperjamin commented 4 years ago

Hi Torsten,

due to tbl2asn requiring a less than 1 year old version, prokka no longer runs. the most recent conda tag for tbl2asn is unfortunately too old. I will open a issue on the bioconda page for this as well, but will leave this one open for others.

kind regards, Casper

tseemann commented 4 years ago

Prokka works correctly in current bioconda. The latest formula uses tbl2asn-forever which does not expire.

conda activate base
conda update --all
conda create -n prokka_env prokka    # or prokka=1.14.6
conda activate prokka_env
prokka --version
ashki23 commented 3 years ago

It looks Conda install option not working very well. 

conda install -c bioconda prokka
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

I have tried this as well:

conda install -c conda-forge -c bioconda -c defaults prokka
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

My conda info output is:

conda info

     active environment : None
            shell level : 0
       user config file : /home/user/.condarc
 populated config files : /home/user/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.8.5.final.0
       virtual packages : __linux=3.10.0=0
                          __glibc=2.17=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /cluster/software/miniconda3  (read only)
      conda av data dir : /cluster/software/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /scratch/user/.conda/pkgs
       envs directories : /scratch/user/.conda/envs
                          /home/.conda/envs
                          /cluster/software/miniconda3/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.5 Linux/3.10.0-1127.8.2.el7.x86_64 centos/7.9.2009 glibc/2.17
                UID:GID : 986055:986055
             netrc file : None
           offline mode : False