Can Jalview run with Java 9


Thank you to everyone who wrote letters of support last year for our application to the BBSRC, we should hear the outcome in the next couple of months.

We are now applying to the Wellcome Trust to renew funding to support Jalview's use in biomedical sequence analysis, including interpretation of genomic variation and long read RNA data (e.g. Nanopore) at the protein coding level. If you would like Jalview to continue to develop and be supported then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to:
support_jalview@bartongroup.org by Friday 22nd March 2019.

Thank you!

Jalview is compatible with Java 9, but only via webstart, or with a modified command-line launch script. If you use the InstallAnywhere version of Jalview it will recommend you install Java 8.

If you have installed Jalview via InstallAnywhere and you cannot access JABAWS services (a dialog box appears after you start Jalview about this), then you can patch the Jalview installation.

On OSX: - Add two lines to the Jalview.app/Contents/Info.plist file after the line starting <string>-Xdock:icon=

                                <string>--add-modules=java.se.ee</string>
                                <string>--illegal-access=warn</string>

On Windows: Open the Jalview.lax file in Notepad (or another editor) # and locate and replace the existing lax.nl.java.option.additional line with

lax.nl.java.option.additional=--add-modules=java.se.ee --illegal-access=warn

Launching Jalview from the command line on Java 9

To run Jalview 2.10.3 on Java 9, you need to add two additional JVM command line arguments:

 --add-modules=java.se.ee --illegal-access=warn

Java 9 also ignores the 'java.ext.dirs' property so instead we recommend launching jalview via a script like:

# set install path of jalview
JALVIEWDIR=$DIR;  # change $DIR to where you built Jalview
# compile the classpath
CLASSPATH=`echo $JALVIEWDIR/*.jar | sed -e 's/r /r:/g'`
# launch Jalview
# you might also want --Xmx<memory in GB>G 
java -classpath $CLASSPATH --add-modules=java.se.ee --illegal-access=warn jalview.bin.Jalview ${@};
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