Thanks Ben. I was able to get Jalview to launch by other users with the method you’ve described.
So far so good.
My next problem is getting Jalview to accept a sequence alignment file on the command line eg.
java -jar jalview-all-2.11.1.0-j1.8.jar drr206pro_mafft.fsa
(I’m bypassing the script to eliminate possible shell artifacts with command line parameters.)
When I run this command, Jalview opens with the Ferredoxin demo, and doesn’t read my sequence file.
I can read this file perfectly well using File → Input Alignment → From file, so the file is good.
I also tried the -fasta switch, but that looks like it’s meant for writing output files.
I was able to get this to work with the most recent version that I installed with the installer, but
that had the problem that other users couldn’t use Jalview.
Since our bioinformatics core uses a GUI interface to launch programs with sequences as input, it is
a bit of a show stopper if we can’t get this to work.
Your help is appreciated.
====================================================
Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB R3T 2N2 CANADA
Phone: 204-474-6085
FAX: 204-474-7528
frist@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~frist/
It is much easier to ask for forgivness than to
ask for permission.
- Bob’s Pragmatic Rules of Order
===========================================================
From: Brian Fristensky
Sent: July 9, 2020 11:07
To: brianfristensky@gmail.com
Subject: Fw: Jalview on multiuser systems
====================================================
Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB R3T 2N2 CANADA
Phone: 204-474-6085
FAX: 204-474-7528
frist@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~frist/
It is much easier to ask for forgivness than to
ask for permission.
- Bob’s Pragmatic Rules of Order
===========================================================
From: Benedict Soares (Staff) <b.soares@dundee.ac.uk>
Sent: July 8, 2020 19:24
To: Brian Fristensky; jalview-discuss@jalview.org
Subject: Re: Jalview on multiuser systems
Caution: This message was sent from outside the University of Manitoba. |
Hi Brian,
You are right that our current linux/unix installers are really designed to be installed into the user’s own space, and as such do not work as a system installation.
We have started work on getting Jalview into mainstream linux packaging systems to allow easy system installation and updates, but unfortunately this is not imminent!
However there are some options you can follow for making a system installation for multiple users.
First suggestion:
To make a system installation available to all users, you could
- Download the “Jalview executable .jar file”:
Go to http://www.jalview.org/getdown/release/ and click on the “View all platforms” link, you should then get all options including the executable .jar.
(The direct link is http://www.jalview.org/getdown/release/jalview-all-2.11.1.0-j1.8.jar)
Put that in, e.g. /opt/jalview/lib/ and make sure it’s globally readable (it doesn’t have to be executable!)
- Ensure you have a system Java 8 Runtime Environment installed. Whether this is present by default and how to install it will depend on your linux distribution and version.
For example, in Ubuntu 20.04 you will need to run
sudo apt install openjdk-8-jre
which then installs into /usr/lib/jvm/java-8-openjdk-amd64
If you want to install a Java 8 JRE specifically for Jalview, we’d recommend getting the latest one from https://adoptopenjdk.net/ which you can unpack in e.g. /opt/jalview/jre8/
- Make a small launcher shell script called “jalview”, something like this 3-liner (change the paths to suit)
#!/usr/bin/env bash
JAVA=/usr/lib/jvm/java-8-openjdk-amd64/bin/java
$JAVA -jar /opt/jalview/lib/jalview-all-2.11.1.0-j1.8.jar $*
in e.g. /opt/jalview/bin/ and make it globally executable.
Users should then be able to launch Jalview with
/opt/jalview/bin/jalview
or you could link to it from somewhere likely to be already in their PATH such as /usr/local/bin so they just need to run
jalview
from the command line.
Notes:
Even if you already have a system Java 8 installed, it’s worth putting the full path to that java binary in the script to ensure that the user runs Jalview with Java 8 and not a more recent (or older) Java they might have on their PATH.
The jalview-all.jar file contains all Java library dependencies so you shouldn’t need anything else installed/downloaded.
This method of installation misses a few niceties such as file associations, desktop icons and automatic updates which the individual installer provides, but it does still have automatic memory setting.
If you want to try out the Java 11 version of Jalview (which is still technically in beta, although being used fairly widely) then use the following jar instead
http://www.jalview.org/getdown/release/jalview-all-2.11.1.0-j11.jar
and obviously make sure you have a Java 11 JRE installed.
Second suggestion:
If your users are familiar with Conda then there are instructions for installing Jalview via bioconda at the bottom of the Jalview download page http://www.jalview.org/getdown/release/. This also uses the jalview-all jar file so might be runnable by all users from a single installation (I haven’t tested this).
Finally, if you want to keep up to date with where we are with linux/unix system installers there are a few issues on our issue tracker you might be interested in:
https://issues.jalview.org/browse/JAL-3520
https://issues.jalview.org/browse/JAL-3620
https://issues.jalview.org/browse/JAL-3631
Hopefully the first suggestion above will be sufficient – let me know how you get on or if you have any problems, and we can add this as an FAQ until there are proper linux packages available.
Best wishes,
Ben
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Brian Fristensky <Brian.Fristensky@umanitoba.ca>
Sent: 08 July 2020 19:42
To: jalview-discuss@jalview.org <jalview-discuss@jalview.org>
Subject: [Jalview-discuss] Jalview on multiuser systems
I am trying to get Jalview 2.11.1.0 to run on a multiuser Linux system.
The problem seems to be that Jalview requires write access to the Jalview home directory, both for writing log files, and for installing updates.
It runs perfectly if I login to the account in which Jalview was installed, but if I try to launch it as another user, I get the Jalview splash window, but the progress bar never does anything.
%jalview
2020/07/08 13:03:59:043 WARNING Unable to redirect output to ‘/home/birch/BIRCH/lib-linux-x86_64/Jalview/launcher.log’: java.io.FileNotFoundException: /home/birch/BIRCH/lib-linux-x86_64/Jalview/launcher.log (Permission denied)
2020/07/08 13:03:59:045 INFO Using appdir from command line: /home/birch/BIRCH/lib-linux-x86_64/Jalview/
2020/07/08 13:03:59:045 INFO Using appid from command line: jalview
2020/07/08 13:03:59:045 INFO Starting …
2020/07/08 13:03:59:047 INFO ------------------ VM Info ------------------
2020/07/08 13:03:59:047 INFO – OS Name: Linux
2020/07/08 13:03:59:047 INFO – OS Arch: amd64
2020/07/08 13:03:59:048 INFO – OS Vers: 4.15.0-106-generic
2020/07/08 13:03:59:048 INFO – Java Vers: 1.8.0_242
2020/07/08 13:03:59:048 INFO – Java Home: /home/birch/BIRCH/lib-linux-x86_64/Jalview2.11.1.0/jre
2020/07/08 13:03:59:053 INFO – Install4j Vers: null
2020/07/08 13:03:59:054 INFO – Install4j Template Vers: 2.11.1.0_F10e9b8be_C30119dce1
2020/07/08 13:03:59:054 INFO – User Name: frist
2020/07/08 13:03:59:054 INFO – User Home: /home/frist
2020/07/08 13:03:59:054 INFO – Cur dir: /home/frist
2020/07/08 13:03:59:055 INFO – Launcher version: 1.8.3-1.2.4_JVL
2020/07/08 13:03:59:055 INFO – startupFilesParameterString:
2020/07/08 13:03:59:055 INFO ---------------------------------------------
2020/07/08 13:03:59:137 INFO Getdown starting [version=1.8.3-1.2.4_JVL, built=2020-04-02 14:45]
2020/07/08 13:03:59:435 INFO Keep on top set to [keep_on_top=true]
2020/07/08 13:03:59:509 INFO Displaying instant background image
2020/07/08 13:03:59:518 WARNING Tried to invokeAndWait but couldn’t. Going to invokeLater instead [Exception=null]
I have tried:
jalview --noquestionnaire --nonews
with the same result. Snooping around the various configuration files doesn’t show anything that looks like it might
help.
Is there a way for users to launch Jalview without write access to the application directory?
The alternative seems to be that each user would have to install Jalview independently.
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