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liaochenlanruo / pgcgap

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
GNU General Public License v3.0
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Unable to install PGCGAP #1

Closed oisinskinnader closed 3 years ago

oisinskinnader commented 3 years ago

After install conda and using the following commands: $conda config --add channels defaults $conda config --add channels bioconda $conda config --add channels conda-forge

I created a pgcgap environment for the installation of PGCGAP. $conda create -n pgcgap python=3 Activated the pgcgap environment. $conda activate pgcgap However, during Installation of PGCGAP using: $conda install pgcgap I get the following issue:

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 each other:

Output in format: Requested package -> Available versions

Where am I going wrong? What should I do?

Thanks,

Oisin

liaochenlanruo commented 3 years ago

After install conda and using the following commands: $conda config --add channels defaults $conda config --add channels bioconda $conda config --add channels conda-forge

I created a pgcgap environment for the installation of PGCGAP. $conda create -n pgcgap python=3 Activated the pgcgap environment. $conda activate pgcgap However, during Installation of PGCGAP using: $conda install pgcgap I get the following issue:

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 each other:

Output in format: Requested package -> Available versions

Where am I going wrong? What should I do?

Thanks,

Oisin

conda install pgcgap=1.0.30

conda remove -n pgcgap --all

and then run:

conda create -n pgcgap pgcgap

oisinskinnader commented 3 years ago

After install conda and using the following commands: $conda config --add channels defaults $conda config --add channels bioconda $conda config --add channels conda-forge I created a pgcgap environment for the installation of PGCGAP. $conda create -n pgcgap python=3 Activated the pgcgap environment. $conda activate pgcgap However, during Installation of PGCGAP using: $conda install pgcgap I get the following issue: 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 each other: Output in format: Requested package -> Available versions Where am I going wrong? What should I do? Thanks, Oisin

  • Have a try with the following command:

conda install pgcgap=1.0.30

  • or remove the pgcgap environment with the command:

conda remove -n pgcgap --all

and then run:

conda create -n pgcgap pgcgap

  • If it does not work, please let me know.

Here is how it went: **(pgcgap) C:\Users\oisin>conda install pgcgap=1.0.30 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 each other:

Output in format: Requested package -> Available versions

(pgcgap) C:\Users\oisin>conda remove -n pgcgap --all

CondaEnvironmentError: cannot remove current environment. deactivate and run conda remove again

(pgcgap) C:\Users\oisin>conda create -n pgcgap pgcgap WARNING: A conda environment already exists at 'C:\Users\oisin\miniconda3\envs\pgcgap' Remove existing environment (y/[n])? y

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 abort. failed

UnsatisfiableError:**

Not really sure what the problem is.

liaochenlanruo commented 3 years ago

@oisinskinnader

oisinskinnader commented 3 years ago

@oisinskinnader

  • Before you remove an environment, you should first deactivate it. So what you need to do is shown as following:
conda deactivate pgcgap
conda remove -n pgcgap --all
conda create -n pgcgap pgcgap

No, I did try deactivate it but got the following:

(pgcgap) C:\Users\oisin>conda deactivate pgcgap deactivate does not accept arguments remainder_args: ['pgcgap']

I think did those commands but to no avail.

liaochenlanruo commented 3 years ago

@oisinskinnader Sorry, please type

"conda deactivate" instead of "conda deactivate pgcgap"

oisinskinnader commented 3 years ago

@oisinskinnader Sorry, please type

"conda deactivate" instead of "conda deactivate pgcgap"

Yeah that worked but there's still problems.

(pgcgap) C:\Users\oisin>conda deactivate

(base) C:\Users\oisin>conda remove -n pgcgap --all

DirectoryNotACondaEnvironmentError: The target directory exists, but it is not a conda environment. Use 'conda create' to convert the directory to a conda environment. target directory: C:\Users\oisin\miniconda3\envs\pgcgap

(base) C:\Users\oisin>conda create -n pgcgap pgcgap WARNING: A directory already exists at the target location 'C:\Users\oisin\miniconda3\envs\pgcgap' but it is not a conda environment. Continue creating environment (y/[n])? y

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 abort. failed

UnsatisfiableError:

liaochenlanruo commented 3 years ago

@oisinskinnader Do you have any software installed which can be connected remotely to your computer, that I can install PGCGAP for you? Such as teamviewer

oisinskinnader commented 3 years ago

@oisinskinnader Do you have any software installed which can be connected remotely to your computer, that I can install PGCGAP for you? Such as teamviewer

Yes. I just sent you an email about that.

Thanks.

liaochenlanruo commented 3 years ago

@oisinskinnader PGCGAP v1.0.31 is available, I have re-submitted an environmental file to Conda to accelerate installation speed, and there are some instructions to solve the installation problems which can be found at https://liaochenlanruo.github.io/pgcgap/#Installation