Welcome to Exomiser Discussions!

[julesjacobsen]

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[squinker]

Hi, are you accepting Merge Requests at the moment?

I'm interested in building Exomiser locally but the build fails because of these two dependencies:

<dependency>
            <groupId>de.sonumina</groupId>
            <artifactId>javautil</artifactId>
            <version>0.0.1</version>
        </dependency>
        <dependency>
            <groupId>ontologizer</groupId>
            <artifactId>ontologizer</artifactId>
            <version>0.0.1-SNAPSHOT</version>
        </dependency>

Are these available somewhere else?

Thanks

[pnrobinson]

@julesjacobsen we should try to replace these dependencies, they are no longer supported and probably phenol can do whatever we need.

[squinker]

yep that's certainly what the comment in the code says. I'm just curious how people build this locally, do people have cached copies somewhere?

[julesjacobsen]

The repo hosting these has recently been decommissioned and it's not our repo. I hadn't noticed as I have the artifacts in my local m2 repository. You can untar these files: sonumina.tar.gz
into your local .m2 directory and the build should work.

I'll be removing the dependencies in the next release.

[squinker]

Ah thanks Jules.

[squinker]

Thanks for the tar, I did cp -r .m2/repository/ ~/.m2/repository and I can compile now.
I got

[ERROR] java.lang.ClassNotFoundException: org.apache.maven.surefire.junitplatform.JUnitPlatformProvider
[ERROR] org.apache.maven.surefire.booter.SurefireBooterForkException: There was an error in the forked process
[ERROR] java.lang.ClassNotFoundException: org.apache.maven.surefire.junitplatform.JUnitPlatformProvider

But changing the version of maven-surefire-plugin from 3.0.0-M5 to 2.22.2 fixed this

[patrickrshea]

Is there a way to provide a list of variant IDs for Exomiser to blacklist during a run? I've looked through the documentation and source code and saw the ability to whitelist variants, but can I do the opposite? I'm trying to exclude a list of known artifact variants that keep showing up in the output.

[damiansm]

Hi Patrick, There is no specific variant blacklist filter but you can do local allele frequency filtering which will have the same effect. If you don't have the actual local frequencies in your cohort for these variants you could just produce a file with some dummy MAF like 50% and configure application.properties for this file and set LOCAL in the list of filtering sources Best wishes Damian

…

On Thu, Jan 26, 2023 at 10:50 PM patrickrshea ***@***.***> wrote: Is there a way to provide a list of variant IDs for Exomiser to blacklist during a run? I've looked through the documentation and source code and saw the ability to whitelist variants, but can I do the opposite? I'm trying to exclude a list of known artifact variants that keep showing up in the output. — Reply to this email directly, view it on GitHub <#423 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABHO4PEPP7YNKWXCKWAL7L3WUL5UJANCNFSM5P2O6VXQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>