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GunzIvan28 / rMAP

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
GNU General Public License v3.0
20 stars 17 forks source link

Solving environment failed #8

Open lurialeslie opened 2 years ago

lurialeslie commented 2 years ago

Hi Ivan, I am trying to setup rMAP on my macbook M1 Big Sur 11.3. I did the initial step but when I tried to install rMAP with the command "conda env create -n rMAP-1.0 --file rMAP-1.0-macOs-installer.yml" I receive this :

Collecting package metadata (repodata.json): done Solving environment: failed

ResolvePackageNotFound:

Could you advise what I am doing wrong and how to solve this issue?

GunzIvan28 commented 2 years ago

Hi @lurialeslie, Apologies for the delayed response. The development team was trying to test and troubleshoot the issue you rasied.

To start off, the error below:

Solving environment: failed

ResolvePackageNotFound:

could be as a result of intermittent internet disruptions from our experience. The conda installer may fail to resolve the packages when internet gets unstable. We have tested the installer on 2 separate MacBooks in both it worked just fine.

WORKAROUND: We suggest you find a place with very stable and reliable internet and then retry the steps at the installation sequentially. It should solve your issue.

I am also available for a zoom call at your earliest convenience to walk you through any technicalities if need be, feel free to reach out.

Let me know how it goes.

Ivan

lurialeslie commented 2 years ago

Hi @GunzIvan28

Many thanks for your reply. Can I ask indeed further assistance as I am still getting the same issue.

GunzIvan28 commented 2 years ago

@lurialeslie ,

Email me a zoom link via ivangunz23@gmail.com. I am available right now for a call.

Sparrow0hawk commented 2 years ago

So the issue here is that by default the architecture of the new Mac M1s is using arm64 which i'd wager a guess these conda libraries haven't been built against (rather have been built for the old intel macs).

You can install rosetta 2, which is Apple's binary translator tool and use the below commands to get conda to install the libraries using the old intel builds.

To install rosetta 2:

$ softwareupdate --install-rosetta

To install rMAP and force conda to install using intel builds, based in this issue:

$ CONDA_SUBDIR=osx-64 conda env create -n rMAP-1.0 -f rMAP-1.0-MacOs-installer.yml

However, when I try ./rMAP -t 8 -c I get some failures here too and which would probably require changing the shell block within ./rMAP.

Another way around these difficulties might be containerising this tool via Docker. I can look at writing a Dockerfile for this and suggesting in a PR?

GunzIvan28 commented 2 years ago

@Sparrow0hawk,

Thanks for the input. You are right about the rMAP compilation; it has not been tested with the M1 and M2 chips because we have no access to either at the moment. It would be exciting to have this contained within a docker environment. We are currently working on implementing it within nextflow and consequently make it compatible with docker and singularity. If you are familiar this workflow, it would be great to add you as a collaborator.

Let me know if you have some time for it.

Cheers, Ivan

Sparrow0hawk commented 2 years ago

I'd be happy to have a look at containerising this tool. I've used both Docker and Singularity in the past so can definitely aim to get rMAP containers for both.

@Sparrow0hawk,

Thanks for the input. You are right about the rMAP compilation; it has not been tested with the M1 and M2 chips because we have no access to either at the moment. It would be exciting to have this contained within a docker environment. We are currently working on implementing it within nextflow and consequently make it compatible with docker and singularity. If you are familiar this workflow, it would be great to add you as a collaborator.

Let me know if you have some time for it.

Cheers, Ivan

GunzIvan28 commented 2 years ago

@Sparrow0hawk, I just invited you as a collaborator for the project. You can create a branch and do the containerization using it after which we can run through the code sometime and then merge with the main branch.

Let me know how it goes or when you need any anything from our end.

Ivan