Liftover Executable

[Isabella Livingston]

Good afternoon, 

I am trying to download the Mac OS version of the liftover tool and it is downloading as a document. I can't run this, so I was wondering how to approach using the tools through the command line in this case.

I was also wondering about generating a chain file for the California sea lion as dog. This would be GCF_009762305.2 > canfam3. 

Thank you in advance for your help,

Isabella Livingston | she/her/hers

Genetics and Genomics Ph.D.Candidate

Genetics and Genomics Scholar

GAANN Biotechnology Fellow                                            

Dept. of Molecular Biomedical Sciences, College of Veterinary Medicine

North Carolina State University

Raleigh, NC 27695

[Gert Hulselmans]

Hi,

Assuming you have the ARM version of the Mac:

# Download with cURL:

$ curl -O -R 'http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.arm64/liftOver'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 9676k  100 9676k    0     0   419k      0  0:00:23  0:00:23 --:--:--  422k

# Set executable bit.

$ chmod a+x liftOver

If you use a different browser than Safari, like Firefox, downloading the file via a browser would work fine.

You still would need to make the downloaded file executable, with the chmod command.

Cheers,

Gert

Op vr 28 jun 2024 om 20:06 schreef 'Isabella Livingston' via UCSC Genome Browser Public Support <gen...@soe.ucsc.edu>:

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[Luis Nassar]

Thanks for Chiming in, Gert.

Isabella,

Regarding the utility what Gert posted should resolve that part. As far as a California sea dog to canFam3 liftOver, we have generated the file and you can find it here:

https://hgdownload.soe.ucsc.edu/hubs/GCF/009/762/305/GCF_009762305.2/liftOver/GCF_009762305.2ToCanFam3.over.chain.gz

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAF18BxtD_d0u%2B5U8md972QdWpXPjea67otQt8a4AumXiMxLuvg%40mail.gmail.com.