Install hanging

[peflanag]

Hi All,

I am trying to install Roary via Conda install Roary but its been hanging now for the last 3 hours.

Any ideas?

Cheers

[AmayAgrawal]

Hi,

I had the same issue while installing roary using conda. The solution that worked out for me was using mamba to install roary instead of conda. Mamba is a drop-in replacement for conda, offering higher speed and more reliable environment solutions.

If you don't have mamba in your base conda enviroment, just install it in base conda environment using

conda install -c conda-forge mamba

Then after installing mamba, activate your roary environment again. Then type the below commands to install it using mamba:

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
mamba install roary

Using the above approach, I was able to install roary in one go

[peflanag]

Hi Amay, Thanks for this, I am about to try it now! P — Dr. Peter Flanagan Ph.D. M.Sc. B.Sc. Clinical Scientist & Visiting Research Fellow in Clinical Microbiology Irish Mycobacteria Reference Laboratory, LabMed Directorate, St. James's Hospital, Dublin 8, Ireland. Tel: +353 (0)1 415 1951 LinkedIn: http://www.linkedin.com/in/Dr-Peter-Flanagan-Phd ORCID: https://orcid.org/0000-0002-4690-0560 [signature_866047262] From: Amay Agrawal ***@***.***> Reply to: sanger-pathogens/Roary ***@***.***> Date: Friday 4 February 2022 at 13:43 To: sanger-pathogens/Roary ***@***.***> Cc: Peter Flanagan ***@***.***>, Author ***@***.***> Subject: Re: [sanger-pathogens/Roary] Install hanging (Issue #550) Hi, I had the same issue while installing roary using conda. The solution that worked out for me was using mamba to install roary instead of conda. Mamba is a drop-in replacement for conda, offering higher speed and more reliable environment solutions. If you don't have mamba in your base conda enviroment, just install it in base conda environment using conda install -c conda-forge mamba Then after installing mamba, activate your roary environment again. Then type the below commands to install it using mamba: conda config --add channels r conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda mamba install roary Using the above approach, I was able to install roary in one go — Reply to this email directly, view it on GitHub<#550 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AH2XNYOWZD56JACCXKO3UCDUZPJWLANCNFSM5NPCB6WA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[skbrimer]

System: Ubuntu 18.04.5 LTS
Conda version: 4.11.0

I was able to install the roary 3.10.2 package, however when I then tried to update to the 3.12 package it seemed to only update the dependencies and not the verison of roary as well. Post conda update roary resulted with roary's version staying at 3.10.2

[Fla1487]

Dear All,

I have the same problem (I use MacBook Pro M2):

I tried with the suggested code:
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
mamba install roary

Obtaining:
Could not solve for environment specs
The following package could not be installed
└─ roary does not exist (perhaps a typo or a missing channel).

Any idea to sove this trouble?
Thank you in advance