PackagesNotFoundError: The following packages are not available from current channels:

[sahuno]

Hi, i can't install gatk via conda/mamba. couldyou pls help pls see steps that i took

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

install command

bash:iscxf001:/data1/greenbab/users/ahunos/apps/gatk-4.5.0.0 1023 $ conda env create -n gatk -f gatkcondaenv.yml

Channels:
 - conda-forge
 - defaults
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - conda-forge::typing_extensions==4.1.1
  - conda-forge::theano==1.0.4
  - pkgs/main::tensorflow==1.15.0
  - conda-forge::scipy==1.0.0
  - conda-forge::scikit-learn==0.23.1
  - conda-forge::python==3.6.10
  - bioconda::pysam==0.15.3
  - conda-forge::pymc3==3.1
  - conda-forge::pip==21.3.1
  - conda-forge::pandas==1.0.3
  - conda-forge::numpy==1.17.5
  - conda-forge::mkl-service==2.3.0
  - conda-forge::mkl==2019.5
  - conda-forge::matplotlib==3.2.1
  - conda-forge::keras==2.2.4
  - conda-forge::joblib==1.1.1
  - pkgs/main::intel-openmp==2019.4
  - conda-forge::h5py==2.10.0
  - conda-forge::dill==0.3.4

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/conda-forge
  - defaults
  - defaults

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

bash:iscxf001:/data1/greenbab/users/ahunos/apps/gatk-4.5.0.0 1024 $ 

software version

bash:iscxf001:/data1/greenbab/users/ahunos/apps/gatk-4.5.0.0 1024 $ mamba --version
mamba 1.5.7
conda 24.3.0

[gokalpcelik]

Hi @sahuno You might want to ensure that the compute environment is able to connect those repositories without issues.

[sahuno]

i just installed pysam and a few softwares in the list but mamba env create -n gatk -f gatkcondaenv.yml still fails. am i missing something?

mamba env create -n pysam install pysam
mamba activate pysam
mamba install -c conda-forge typing_extensions=4.1.1
mamba install -c conda-forge python=3.6.10
mamba install -c conda-forge pymc3==3.1 -y
mamba install -c conda-forge pip=21.3.1
mamba install -c conda-forge scipy=1.0.0
mamba install -c conda-forge numpy=1.17.5

[gokalpcelik]

We do not have a supported installation medium through mamba. That could be the reason why repositories do not return the needed packages. We recommend installing miniconda and using miniconda to create the environment. If these options don't work for you we also have our docker image with conda environment installed and you may use it if your compute environment permits.