Running Mauve with Java 10 | EdwardsLab EdwardsLab Delivering the best in bioinformatics… Menu Skip to content Home Members Research Press Software Lab GitHub pages Lab Sourceforge Site Lab blog SRA Publications Publications Talks White papers Theses Poster International Join Contact Us Running Mauve with Java 10 They short answer is you can’t (currently) run the totally awesome Mauve with Java 10, but you can probably run Mauve anyway. Here’s how! TL;DR locate java | grep java$ | grep -w bin
export JAVA_CMD=/usr/lib/jvm/java-8-openjdk-amd64/bin/java If you get this error when you try to run the awesome Mauve from Aaron Darling’s lab, its because you have a too new version of Java! $ mauve
[warning] /usr/bin/mauve: No JAVA_CMD set for run_java, falling back to JAVA_CMD = java
Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: "."
at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.base/java.lang.Integer.parseInt(Integer.java:638)
at java.base/java.lang.Integer.parseInt(Integer.java:770)
at org.gel.mauve.gui.Mauve.hasRequiredJVM(Unknown Source)
at org.gel.mauve.gui.Mauve.init(Unknown Source)
at org.gel.mauve.gui.Mauve$2.run(Unknown Source)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue.access$600(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) To fix this, first, you need to find another version of Java. If you’re like me, your computer probably has many different versions of Java, because different software insist on installing their own version to ensure they can run. On a linux machine, you can typically use locate to find another version: locate java | grep java$ | grep -w bin This will list all your java executables. On my laptop I have 11 different versions of Java!! Now you can tell Java which version to use by setting the JAVA_CMD variable: export JAVA_CMD=/usr/lib/jvm/java-8-openjdk-amd64/bin/java This one uses Java 8 from the openjdk installation I have. With this command, mauve will now start just fine. Good luck! Related This entry was posted in Lab blog and tagged bash, mauve on August 12, 2018 by Rob Edwards. Post navigation ← phage terminase orientation How to mess with BLAST results → Contact Information for Rob Edwards Office: PS 123 Lab: PS 106 Phone: +1 619 594-1672 Fax: +1 619 594 6746 Email: redwards@sdsu.edu Search for: Log In & RSS Log in Entries feed Comments feed WordPress.org Proudly powered by WordPress
