Package Details: jalview 2.10.1-1

Git Clone URL: https://aur.archlinux.org/jalview.git (read-only)
Package Base: jalview
Description: Bioinformatics Multiple Alignment Editor
Upstream URL: http://www.jalview.org/
Licenses: GPL3
Submitter: semi
Maintainer: semi (sebstar)
Last Packager: semi
Votes: 9
Popularity: 0.000055
First Submitted: 2011-09-01 15:08
Last Updated: 2017-05-13 10:38

Latest Comments

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 jalview.org 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

@sebstar
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
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,20 +1,20 @@
# Maintainer: Stefan Seemayer <mail@semicolonsoftware.de>
pkgname=jalview
-pkgver=2.9.0b2
+pkgver=2.10.1
pkgrel=1
pkgdesc="Bioinformatics Multiple Alignment Editor"
arch=(any)
url="http://www.jalview.org/"
license=('GPL3')
depends=(java-runtime)
-makedepends=(perl wget)
+makedepends=(wget xmlstarlet)

source=( "http://www.jalview.org/webstart/jalview.jnlp"
"logo.gif"
"jalview"
"jalview.desktop")

-md5sums=('3047b069458cfddd0f598b3bf65ba15d'
+md5sums=('0ce946664997d3cfceab7cf7a639f8ba'
'e124f66d646560813b1a06b0cff02d3a'
'0ea5c6990bfa050c9c69f24926da3d57'
'b3a842500e7ff3cd1324dede69822d21')
@@ -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 $jars; do
wget "http://www.jalview.org/webstart/$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

md5sums=('22199389866d5ea6829d5005bed6974c'
'e124f66d646560813b1a06b0cff02d3a'
'0ea5c6990bfa050c9c69f24926da3d57'
'b3a842500e7ff3cd1324dede69822d21')

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.

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