Package Details: hmmer3-2 3-1

Git Clone URL: https://aur.archlinux.org/hmmer3-2.git (read-only)
Package Base: hmmer3-2
Description: Profile hidden Markov models (HMMs) for database searching using consensus sequences containing the version 2 and 3 implementations.
Upstream URL: http://hmmer.org/
Licenses: GPL
Conflicts: hmmer, hmmer2
Provides: hmmer, hmmer2
Submitter: anadon
Maintainer: anadon
Last Packager: anadon
Votes: 0
Popularity: 0.000000
First Submitted: 2018-03-01 21:22
Last Updated: 2018-03-01 21:22

Dependencies (6)

Required by (9)

Sources (2)

Latest Comments

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anadon commented on 2019-03-21 14:26

@Kunda The eddylab link does not go to a version which supports installations of hmmer versions 2 and 3. That is the whole point of this package.

I'm in the process of re-coding hmmer2 entirely in my free time, but it is going to take a while. The same practice which necessitated this package means there are some rather massive cleanups to undertake.

Kunda commented on 2019-03-21 14:19

http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz

anadon commented on 2018-04-03 16:52

Got the repo added, and will be applying patches soon.

anadon commented on 2018-03-22 20:47

Meeting got pushed back.

anadon commented on 2018-03-07 14:10

Meeting to open a repo at Michigan Technological University's github will happen March 19th.

anadon commented on 2018-03-06 00:15

There are a couple of hidden options, one of which is multi-threading. Today I got the basics of all that working, cleaned up, and the executable names differently. I'll be throwing up the repo tomorrow and track down users of this older package.

anadon commented on 2018-03-05 15:11

It looks like Sean Eddy is unwilling to make his tools easy to set up and use, so I think I'm going to fork them, fix it, and update people that it exists. I want it to be more easily packaged and available on more distributions.

anadon commented on 2018-03-03 18:14

I needed this for work Thursday, so I just went ahead and got something up and out here. Regardless, Sean Eddy should do something to help prevent this situation. There are bound to be a few hundred people a year that deal with this and upstream should make this easier. So lets hold on a few days still while I get this sorted out with them. A few days on a rarely used package that has an easy alternate is probably not an issue and is outweighed by having this all here to compare and contract different approaches, how complex each is, and clear this issue up long term.

mschu commented on 2018-03-03 16:16

I completely agree with the co-installation of packages, which is why I made the changes you proposed in the hmmer2 package (see comments there).

The deletion request was because you made a duplicate package where you maybe should have waited 2 days for the above fix instead of submitting the same thing again. This package is against guidelines, even if it was working.

(And of course you should have checked if your PKGBUILD actually works, but that is not the main point here. - I was being lazy and just copied the comment)

NB: It's not my intention to be rude here, but I think the points are valid

anadon commented on 2018-03-02 18:12

Talked with Sean Eddy's lab, and a meeting is set for Monday. I hope to sort these issues out then.