Package Details: hhsuite 3.0.beta.3-1

Git Clone URL: https://aur.archlinux.org/hhsuite.git (read-only)
Package Base: hhsuite
Description: A set of programs for protein sequence homology detection by iterative HMM-HMM comparison for computational biology like PSI-BLAST
Upstream URL: https://github.com/soedinglab/hh-suite
Keywords: bioinformatics hh-suite homology search
Licenses: GPL
Submitter: None
Maintainer: semi
Last Packager: semi
Votes: 1
Popularity: 0.000000
First Submitted: 2012-02-28 23:52
Last Updated: 2018-01-07 15:12

Latest Comments

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semi commented on 2018-01-07 15:14

Updated to 3.0-beta3

@apolih: If you or someone else wants to provide such packages, I would be happy to reference them in this package.

apolih commented on 2017-05-08 18:13

Thanks for providing this package. I have a few suggestions as I have tried to run it:

could use optional dependency on a (not yet existing) blast-legacy-bin package with files from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.9/ which are needed to run the addss.pl script

likewise for a psipred-bin package with files from http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/

then patch HHPaths.pm to point to directories from those packages

semi commented on 2016-11-01 16:23

Updated to 3.0 beta 2

semi commented on 2016-02-15 12:17

Fixed.

semi commented on 2016-02-15 07:12

I just got a notification that the upstream download link has died. I'm in contact with the upstream authors on where to point the PKGBUILD, please stay tuned until then.

semi commented on 2014-02-27 09:05

Updated package to configure PERLLIB and HHLIB correctly so bundled scripts work out of the box.

semi commented on 2013-03-22 16:14

Updated to 2.0.16

semi commented on 2013-02-04 11:26

Updated to the new version 2.0.15

Anonymous comment on 2013-02-04 11:26

Disown for adoption.

Anonymous comment on 2012-12-18 16:03

Hi there,
Looks like you're missing a couple of versions, and the source URL has changed. I've included an updated PKGBUILD and a patch that includes unistd.h in hhsearch.

PKGBUILD:
pkgver=2.0.15
...
source=(use_unistd.patch ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/releases/$pkgname-$pkgver.tar.gz)

build()
{
cd $srcdir/$pkgname-$pkgver/
patch -Np0 -i ../use_unistd.patch
make all WITH_NATIVE=1 NO_PNG=1
}
...
md5sums=('cab3b8f636c2fda4a459bbe4bee57fc3' 'f995aeceb710715d6ebd4e1fed6df5db')

use_unistd.patch:
--- src/hhsearch.C 2012-06-15 16:00:13.000000000 +0100
+++ src/hhsearch.C 2012-12-18 15:49:24.726997376 +0000
@@ -44,6 +44,7 @@
#include <errno.h> // perror()
#include <cassert>
#include <stdexcept>
+#include <unistd.h> // access(), R_OK

#ifdef PTHREAD
#include <pthread.h> // POSIX pthread functions and data structures