Package Details: jalview 2.10.5-1

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Package Base: jalview
Description: Bioinformatics Multiple Alignment Editor
Upstream URL:
Licenses: GPL3
Submitter: semi
Maintainer: semi
Last Packager: semi
Votes: 11
Popularity: 0.000002
First Submitted: 2011-09-01 15:08
Last Updated: 2019-04-06 13:57

Required by (0)

Sources (54)

Latest Comments

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sebstar commented on 2017-04-20 11:10

Current PKGBUILD fails with 2.10 because it misses the jalview.jar (and includes MacOS jars). Here's a fixed version, using xmlstarlet:

diff --git a/PKGBUILD b/PKGBUILD
index 459ec26..4e56d6f 100644
@@ -1,20 +1,20 @@
# Maintainer: Stefan Seemayer <>
pkgdesc="Bioinformatics Multiple Alignment Editor"
-makedepends=(perl wget)
+makedepends=(wget xmlstarlet)

source=( ""

@@ -24,8 +24,8 @@ build() {
mkdir -p "$srcdir/$pkgname-$pkgver" || exit 1
cd "$srcdir/$pkgname-$pkgver" || exit 1

- # parse list of jar files from JNLP file
- jars=$(perl '-ne /<jar href="([^"]*)"\/>/ && print "$1\n"' "$srcdir/jalview.jnlp")
+ # parse list of jar files from JNLP file, excluding MacOS jars
+ jars=$(xmlstarlet sel -t -m '/jnlp/resources[not(@os)]/jar' -v '@href' -n "$srcdir/jalview.jnlp")

for jar in $jars; do
wget "$jar" -O "$jar" || exit 1

semi commented on 2015-11-06 07:12

Updated to 2.9.0b2

semi commented on 2015-04-29 09:32

Apologies for the very delayed update - updated to 2.8.2

confusedfla commented on 2014-12-20 00:05

(jalview released 2.8.2)

confusedfla commented on 2014-12-20 00:04

please update the md5sum for the jalview.jnlp


Rhinoceros commented on 2014-06-08 01:58

I'm using Kwin/KDE. I've only just moved to Arch, so I've not tried the 2.8.0 version before. (I never had these problems in Kubuntu, although I'm not sure what version I ran.) I get the same glitches using the Java Web Start version.

I'm certainly happy to test removal of JGoogleAnalytics_0.3.jar at least, once I get Jalview working. I guess a potential problem is that removal of some components might break obscure parts of Jalview that I don't use, for others.

semi commented on 2014-06-06 09:24

Hmm, it seems to work fine on my system (OpenJDK 1.7.0_55 on AwesomeWM). What window manager are you using? Did this problem occur with the 2.8.0 version? Does the problem also occur when you launch the JalView Desktop from their homepage via Java Web Start (the purple button on

The jar files included in the installation are all the ones listed in the JNLP file. I'm not sure if this is the minimal required set but if anyone is willing to try removing some of them and test if Jalview still runs, I'd be happy to remove them from the build :)

Rhinoceros commented on 2014-06-06 03:59

It builds fine, but after launching there are many graphic glitches, making it unusable. (See screenshot ) I get this for openJDK (1.7.0_55) and Oracle Java (Java version: 1.7.0_60).

Also, I'm not sure if it's necessary, but the build installs in a whole lot of files such as /usr/share/java/jalview/JGoogleAnalytics_0.3.jar

semi commented on 2014-06-05 08:26

The download links for both the source package and the installer that I've used so far to build the package are still on 2.8.0. I had to create a new build strategy that will parse the jar filenames from the JNLP file for the Jalview Desktop link. Hopefully this will work for everybody - feedback is appreciated :)

Rhinoceros commented on 2014-06-05 05:11

Newest version is 2.8.1.