Package Details: jalview 2.10.3-4

Git Clone URL: (read-only)
Package Base: jalview
Description: Bioinformatics Multiple Alignment Editor
Upstream URL:
Licenses: GPL3
Submitter: semi
Maintainer: semi (sebstar)
Last Packager: sebstar
Votes: 11
Popularity: 1.028889
First Submitted: 2011-09-01 15:08
Last Updated: 2018-05-05 16:34

Required by (0)

Sources (53)

Latest Comments

iosonofabio commented on 2018-05-31 22:02

outdated sha256sums:

jalview.jar: a7d39e0635db898ab1526e667bf0d0b8f6b90ce6267cfe3c8e4015fdfaed7947

jalview_jnlp_vm.jar: d20da415c23252ce1df138ec1becfd7b4f3b3c8770c1c1040e870867fcd9a4a8

sebstar commented on 2018-05-05 16:35

thanks for the script! I bumped the package to pkgrel 4. Oddly, I had to remove the leading ../ in front of the source files for the install commands.

squirrel42 commented on 2018-01-26 22:09

All of the .jar files currently fail the validity check for me.

semi commented on 2018-01-07 14:53

Updated to 2.10.3 - Sorry for the long delay.

@sebstar Agreed about your security concerns. There is now a python script included in the repo that will inspect the JNLP file, download the JARs, compute checksums and update the PKGBUILD with the new checksums and URLs. I've also switched to a less bruteforceable SHA256.

Rhinoceros commented on 2018-01-07 11:39

Bump. If there's no response, I'll file an orphan request and fix it myself.

Rhinoceros commented on 2017-10-26 01:15

jalview.jnlp is failing the checksum for me. Is anyone else having this problem? I tried downloading it several times.

sebstar commented on 2017-05-13 12:04

@semi, thank you. There's a couple more problems that we should address:
1) We don't use https. Well, we can't at the moment, because has an invalid certificate for their domain. I wrote them to please fix their certificate. Hosting jars over http is ridiculously dangerous in today's environment.
2) Ditch md5 and generate SHA256 and SHA512 checksums.
3) Instead of dynamically generating the list of jars to download with xmlstarlet, actually put this list in the source array. Makes the package more secure, as all jars' checksums would be included.

semi commented on 2017-05-13 10:39

@sebstar, I've added you as a Co-maintainer if you are interested

semi commented on 2017-05-13 10:38

Finally updated with thanks to @sebstar

eNauz commented on 2017-04-21 07:00

Thank you, this worked like a charm!

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.

Rhinoceros commented on 2014-06-05 05:11

Newewst version is 2.8.1.

semi commented on 2011-10-17 16:10

Updated - I just wasn't on e-mail for a few days, I still have time to maintain the package. Thanks for the offer :)

iosonofabio commented on 2011-10-13 17:02

Please update the MD5 hash.

If you have no time or interest in the package anymore, please disown it and I'll adopt it. Thanks.