Update Muscle to v5

[jamesabbott]

Muscle v5 was released a number of years ago, and claims to be bigger/better/faster etc., but has CLI changes which are incompatible with the existing v3.8.

Both jabaws and slivka are still using 3.8, but this is probably a good opportunity to migrate to v5: https://drive5.com/muscle/

[foreveremain]

Recommend a distinct service is created.. ISTR we discussed how to handle distinct versions of tools (as opposed to distinct versions of service definitions), but can't remember if we came to a conclusion about how to do it beyond the obvious structured service name/version approach.

On Tue, 6 Aug 2024, 13:00 James Abbott, @.***> wrote:

Muscle v5 was released a number of years ago, and claims to be bigger/better/faster etc., but has CLI changes which are incompatible with the existing v3.8.

Both jabaws and slivka are still using 3.8, but this is probably a good opportunity to migrate to v5: https://drive5.com/muscle/

— Reply to this email directly, view it on GitHub https://github.com/bartongroup/slivka-bio/issues/8, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJ7SW4O7OUJHP4YASPGRCDZQC3HDAVCNFSM6AAAAABMCFWL32VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ2TANZQG42TMOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[stuartmac]

So muscle5 and muscle3 services?

One added complication is that we'll need separate conda envs for that. This is fine, but will add extra complexity to slivka-bio installation and configuration. Perhaps we could put muscle5 in the "slivka" environment and have additional instructions for people who want muscle3 too?

@jamesabbott mentions we can also build from source and name the binaries accordingly

[warownia1]

If we want two versions of any tool from bioconda, we can no longer have _slivkabio conda package. If users start installing tools in other environments then the solution is no longer portable. But, do we really need to have two versions of muscle in slivka-bio? I think, this repo along with the conda package is meant to be a quick and easy way to get started with slivka. This is not the same version that is running on our cluster. There, we can (and should) have multiple versions of tools.

[jamesabbott]

This is all a bit of a pain of bioconda's own making. Different maintainers have taken different approaches - when mummer 4 was released which had an incompatible CLI with mummer 3, it was added as 'mummer4' rather than a new major version of mummer, while installing 'muscle' gives you a random CLI depending upon which version the resolver favours. Combined with their preference for minimising version pinning it isn't really helping reproducible environments.

I agree that while we may need multiple services for our own porpoises, for the general population a consistent and reproducible installation is essential, and I would expect that would include the latest available stable releases.

From: Mateusz Warowny @.> Date: Tuesday, 6 August 2024 at 17:25 To: bartongroup/slivka-bio @.> Cc: James Abbott (Staff) @.>, Mention @.> Subject: Re: [bartongroup/slivka-bio] Update Muscle to v5 (Issue #8)

CAUTION: This email originated from outside the University of Dundee. Do not click links or open attachments unless you recognise the sender's email address and know the content is safe.

If we want two versions of any tool from bioconda, we can no longer have slivka_bio conda package. If users start installing tools in other environments then the solution is no longer portable. But, do we really need to have two versions of muscle in slivka-bio? I think, this repo along with the conda package is meant to be a quick and easy way to get started with slivka. This is not the same version that is running on our cluster. There, we can (and should) have multiple versions of tools.

— Reply to this email directly, view it on GitHubhttps://github.com/bartongroup/slivka-bio/issues/8#issuecomment-2271680680, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABIRXSPCIUTS5VAEVGFTASDZQD2HNAVCNFSM6AAAAABMCFWL32VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZRGY4DANRYGA. You are receiving this because you were mentioned.Message ID: @.***>

The University of Dundee is a registered Scottish Charity, No: SC015096

[warownia1]

I can update it to work with align and super5 commands, but I need help with methods to manipulate ensembles.