Hey Brian. -open is the key argument here. -h will give you some hints.
By the way.. did you consider the bioconda package for managing jalview installs? J. On Thu, 9 Jul 2020, 21:36 Brian Fristensky, <brian.fristen...@umanitoba.ca> wrote: > 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 > fr...@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:* brianfristen...@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 > fr...@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.soa...@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 > 1) 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!) > 2) 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/ > 3) 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-boun...@jalview.org < > jalview-discuss-boun...@jalview.org> on behalf of Brian Fristensky < > brian.fristen...@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. > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss >
_______________________________________________ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
