Question: Error when trying to run IGV on server
0
gravatar for kristina.mahan
9 months ago by
kristina.mahan50 wrote:

I want to use IGV on a server so I don't have to download bam files to my local machine. I used conda to install igvtools. When I type igvtools in the command line I get this error:

Using system JDK. Unrecognized option: --module-path=/home/kmmahan/miniconda3/envs/igv/share/igvtools-2.5.3-0/lib Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

  1. Can igv be used on a server
  2. How do you launch igv once it is installed on a server
  3. What are these errors?

Any help would be appreciated

igv • 783 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by kristina.mahan50
1

I am pretty sure that igvtools is not the same thing as IGV.

ADD REPLYlink written 9 months ago by steve2.5k

Command line version of IGV includes igvtools. That package requires Java 11.

ADD REPLYlink written 9 months ago by genomax85k

IGV can be used on a server. Do you have java installed on this server? IGV needs Java. Local installs require Java 11.

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax85k

(igv) [kmmahan@blogin4 analysis]$ java -version openjdk version "1.7.0_91" OpenJDK Runtime Environment (Zulu 7.12.0.3-linux64) (build 1.7.0_91-b15) OpenJDK 64-Bit Server VM (Zulu 7.12.0.3-linux64) (build 24.91-b15, mixed mode)

So it is using JDK instead of JVM?

ADD REPLYlink written 9 months ago by kristina.mahan50

I am guessing that 1.7 is based on Java 7? If thats the case you will need to update this.

ADD REPLYlink written 9 months ago by steve2.5k
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