Package Details: jalview 2.10.3-3

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: 0.000000
First Submitted: 2011-09-01 15:08
Last Updated: 2018-01-07 14:55

Required by (0)

Sources (54)

Latest Comments

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 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

All comments