Help solve the issue of running the tool in our HPC system

[Yang, Jingjing]

Hi,

I am having trouble running the LiftOver standalone tool in our HPC system. I have the following errors, and it won't be possible for us to get higher version of the GLBC in our current system. I am wondering if you could share the source code, so that we could built one by ourselves. Or if you could help build one for Rocky Linux 8 ? Thanks a lot.

./liftOver: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./liftOver)

./liftOver: /lib64/libcurl.so.4: no version information available (required by ./liftOver)

./liftOver: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by ./liftOver)

./liftOver: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by ./liftOver)

./liftOver: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by ./liftOver)

*******************************
Jingjing Yang, Ph.D.
Associate Professor of Human Genetics
Center for Computational and Quantitative Genetics

Department of Human Genetics
Emory University 

Office: Whitehead Biomedical Research Building, Suite 305K
Office Phone: 404-727-3481
YangLabWeb: https://yanglab-emory.github.io/

 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

We have a set of v479 binaries that you can download that do not require an updated GLIBC library. I hope these work for your purposes, and please let us know if you run into any issues.

https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v479/

If the v479 binaries don't meet your needs, we can assist you with any issues you may have compiling from source. The userApps.src.tgz were intended to be built from source, and we can guide you through the process if needed.

https://hgdownload.soe.ucsc.edu/admin/exe/userApps.src.tgz

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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[Yang, Jingjing]

The v479 binary file works. Thanks a lot for your help.

*******************************
Jingjing Yang, Ph.D.
Associate Professor of Human Genetics
Center for Computational and Quantitative Genetics

Department of Human Genetics
Emory University 

Office: Whitehead Biomedical Research Building, Suite 305K
Office Phone: 404-727-3481
YangLabWeb: https://yanglab-emory.github.io/

 

---

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Thursday, August 14, 2025 7:24 PM
To: Yang, Jingjing <jingji...@emory.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: [External] Re: [genome] Help solve the issue of running the tool in our HPC system

 

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