Cannot install

[pavlo888]

Hi,

I am trying to install the package but apparently Conda cannot find it. Would you please have look at this issue and let me know how to install the pirate package? I am eager to try it out.

Cheers, Pablo

[SionBayliss]

Hi Pablo,

PIRATE relies on the default bioconda channels for installation. I have updated the readme to reflect this.

It should install if you run:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

followed by:

conda install -c sionbayliss pirate 

Could you let me know if that resolves your problems?

All the best, Sion

[pavlo888]

Hi Sion,

Thank you for your fast response. I have run the the commands to activate the specific Conda channels that you suggested. However, it turns out that I already had those channels activated.

Then I ran the install command for pirate and unfortunately it did not work.

This is what I get in the prompt:

(pirate) Pablos-MacBook-Air:pirate_output pablovargas$ conda install -c sionbayliss pirate

Collecting package metadata: done

Solving environment: failed

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

• pirate

Current channels:

• https://conda.anaconda.org/sionbayliss/osx-64

• https://conda.anaconda.org/sionbayliss/noarch

• https://conda.anaconda.org/conda-forge/osx-64

• https://conda.anaconda.org/conda-forge/noarch

• https://conda.anaconda.org/bioconda/osx-64

• https://conda.anaconda.org/bioconda/noarch

• https://repo.anaconda.com/pkgs/main/osx-64

• https://repo.anaconda.com/pkgs/main/noarch

• https://repo.anaconda.com/pkgs/free/osx-64

• https://repo.anaconda.com/pkgs/free/noarch

• https://repo.anaconda.com/pkgs/r/osx-64

• https://repo.anaconda.com/pkgs/r/noarch

• https://conda.anaconda.org/r/osx-64

• https://conda.anaconda.org/r/noarch

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.

(pirate) Pablos-MacBook-Air:pirate_output pablovargas$

Hopefully, you could help me find a solution because I am very interested in trying this package.

Best regards, Pablo

On Mon, May 20, 2019 at 11:22 AM Sion Bayliss notifications@github.com wrote:

Hi Pablo,

PIRATE relies on the default bioconda channels for installation. I have updated the readme to reflect this.

It should install if you run:

conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge

followed by:

conda install -c sionbayliss pirate

Could you let me know if that resolves your problems?

All the best, Sion

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/SionBayliss/PIRATE/issues/6?email_source=notifications&email_token=AK4VSEXFE2ZKTD2EIEFGQVDPWJUW3A5CNFSM4HN5JNI2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVYGZ5I#issuecomment-493907189, or mute the thread https://github.com/notifications/unsubscribe-auth/AK4VSEQJ7X4QCAI3562C5QTPWJUW3ANCNFSM4HN5JNIQ .

[SionBayliss]

Hi Pablo,

The conda installation (and PIRATE in general) was built on a linux operating system. The conda build of PIRATE is currently incompatible with MacOS. Assuming the dependencies are available for MacOS via conda you can install them with:

conda install perl-bioperl==1.7.2 mcl>=14.137 mafft==7.310 cd-hit>=4.6.4 fasttree>=2.1.10 diamond>=0.9.14 blast>=2.2.31 parallel>=20170422

And then git clone the github repo. If the dependencies are in your PATH then the PIRATE executable (/github_repo/bin/PIRATE) should function. I do not have a MacOS machine so I haven't tested this, there maybe compatibility issues between the operating systems.

Please let me know if this works as it may be of use to other users.

[pavlo888]

Hi Sion,

I installed all the dependencies in a conda environment and then used the PIRATE executable while the environment was active. It worked!

Thank you for your support.

Best regards, Pablo

On Wed, May 22, 2019 at 3:55 PM Sion Bayliss notifications@github.com wrote:

Hi Pablo,

The conda installation (and development of PIRATE in general) was built on a linux operating system. The conda build of PIRATE is currently incompatible with MacOS. Assuming the dependencies are available for MacOS via conda you can install them with:

conda install perl-bioperl==1.7.2 mcl>=14.137 mafft==7.310 cd-hit>=4.6.4 fasttree>=2.1.10 diamond>=0.9.14 blast>=2.2.31 parallel>=20170422

And then git clone the github repo. If the dependencies are in your PATH then the PIRATE executable (/github_repo/bin/PIRATE) should function. I do not have a MacOS machine so I haven't tested this, there maybe compatibility issues between the operating systems.

Please let me know if this works as it may be of use to other users.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/SionBayliss/PIRATE/issues/6?email_source=notifications&email_token=AK4VSERE6UFMXIFPJDGCRBLPWVGD7A5CNFSM4HN5JNI2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV7D7TI#issuecomment-494813133, or mute the thread https://github.com/notifications/unsubscribe-auth/AK4VSEVOLESRRQHFQ43QNA3PWVGD7ANCNFSM4HN5JNIQ .

[SionBayliss]

Hi Pablo,

Thanks for the feedback. I am glad it worked. I will update the readme for Mac users.

Cheers, Sion