Package Details: phyml 1:3.2.20160530-1

Git Clone URL: https://aur.archlinux.org/phyml.git (read-only)
Package Base: phyml
Description: Builds phylogenies from DNA or protein sequences using a maximum likelihood approach
Upstream URL: http://www.atgc-montpellier.fr/phyml/
Licenses: GPL2
Submitter: None
Maintainer: mschu
Last Packager: mschu
Votes: 6
Popularity: 0.000847
First Submitted: 2009-04-02 01:54
Last Updated: 2016-11-24 13:55

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Required by (0)

Sources (1)

Latest Comments

Rhinoceros commented on 2015-02-08 01:28

Okay, I've done a bit more homework, and I realised that split packages normally have one build() section, and hence it's probably not a good idea to use a split package in this case.

I've created a new package phyml-mpi, just because it's a bit easier as per reasons in my previous post. Let me know if you want to adopt it, anyway. Cheers.

Rhinoceros commented on 2015-02-02 21:39

Thanks for the fix.

With MPI, configuring upstream phyml with --enable-mpi creates a separate binary phyml-mpi. This does not conflict with phyml. Hence, I attempted to change the package name to phyml-mpi, so I could install both. However, pacaur (for example) won't let me change the package name, although packer does, although this means that packer/pacaur -Syu won't pick up the package in future.

I wonder if there is any disadvantage to compiling with --enable-mpi by default? If so, then perhaps this package could enable this by default, with optdepends openmpi. If it *is* better to install both, another option might be to make phyml a split package, so that users can install/upgrade both without having to download the source twice.

mschu commented on 2015-02-02 13:42

Concerning MPI, just change the option in the PKGBUILD. A separate package is only needed when it's used by more people in my opinion.

mschu commented on 2015-02-02 13:41

You are right, I made a mistake reading the URL and still had the old version cached instead of deleting it.

Should be fixed now (for real).

Rhinoceros commented on 2015-02-02 11:11

It's still 404-ing for me. Isn't it 20141029 that you want? Also, would you consider maintaining phyml-mpi (i.e. multi-threaded)? i.e. just configure it with --enable-mpi? I'm happy to do it otherwise, but might make more sense for you to if you are willing.

mschu commented on 2015-02-02 10:05

It seems the git download URL changed slightly.

Fixed that, and some autoconf issue. Not bumping $pkgrel because it is built from the same source (same md5sum).

Rhinoceros commented on 2015-02-02 03:43

Ugh, apologies. The stable version was released 26 Feb 2014, but is actually from April 2012. However, the current PKGBUILD still 404s.

Rhinoceros commented on 2015-02-02 03:22

When trying to build, phyml-20140926.tar.gz now 404s. Upstream is being strange. The stable release from 23 Feb was deleted, but now there is a stable release from 26 Feb 2014.

https://github.com/stephaneguindon/phyml-downloads/releases

wookietreiber commented on 2014-10-16 12:26

This appears to be the latest version:

https://github.com/stephaneguindon/phyml-downloads/releases/download/development/phyml-20140926.tar.gz

talavis commented on 2014-09-12 11:37

Seems like the current devel version is 20140911 now.

pkgver=20140911
sha1sums=('c554287908951bf3a0cf932a5d65fe3cdcf4453a')

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