search

TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
Other
24 stars 11 forks source link

How do I adjust the version of Exomiser #558

Closed BioHuangDY closed 1 year ago

BioHuangDY commented 2 years ago

Now the version of Exomiser has been upgraded from 12.1.0 to 13.0.1, more than 2 years have passed. I tried to install Exomiser 12.1.0, but kept getting errors. The error is as follows： [ERROR] PROTOC FAILED: ~/software/Exomiser/Exomiser-12.1.0/exomiser-core/target/protoc-plugins/protoc-3.7.0-linux-x86_64.exe: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory

However, when I install Exomiser 13.0.1 I get no errors. But LIRICAL need Exomiser12.1.0. I tried to change the version of Exomiser in pom.xml to 13.0.1, but I still get an error when I install LIRICAL. Can I ask if I use Exomiser 13.0.1 version in LIRICAL？

ielis commented 2 years ago

Hi @BioHuangDY we made a new LIRICAL release today. Despite using the Exomiser variant database in the analysis, the new release does not depend on Exomiser code. Therefore, the build should work on your side now (e.g. the latest master). Can you give it a try?

BioHuangDY commented 2 years ago

Dear Danis: Thank you for your notice. I will try the new version of LIRICAL soon.

Daoyi Huang

发件人: Daniel Danis 发送时间: 2022年7月15日 5:07 收件人: TheJacksonLaboratory/LIRICAL 抄送: BioHuangDY; Mention 主题: Re: [TheJacksonLaboratory/LIRICAL] How do I adjust the version ofExomiser (Issue #558)

Hi @BioHuangDY we made a new LIRICAL release today. Despite using the Exomiser variant database in the analysis, the new release does not depend on Exomiser code. Therefore, the build should work on your side now (e.g. the latest master). Can you give it a try? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

BioHuangDY commented 2 years ago

Sorry to bother you again, I have a new problem. After mvn package, BUILD SUCCESS is also displayed, but there is no LIRICAL.jar file. The installation page mentioned in the README.md file has not been updated, and the /docs/setup.rst file has not been updated, so I have no idea how to use LIRICAL. So I would like to ask if it is possible to rewrite an installation and usage guide?

ielis commented 2 years ago

@BioHuangDY you can download a pre-built JAR file from Releases. However, if you absolutely want to build from source, then this will do the trick:

cd LIRICAL
./mvnw -Prelease clean package