url?

[YonkoBigMom]

Hi,

I am trying to run the demo code

hotspot3d uppro --measure average --output-dir prep/ --pdb pdb/ --gene-file demo.maf --parallel local --max-processes 6 1>demo.uppro.out 2>demo.uppro.err

and it gave the error:

HotSpot3D::HugoGeneMethods::makeHugoGeneObjects ERROR: no data from url request.

Any ideas how to fix this?

Thanks

[wangweifeng2018]

hi, YonkoBigMom.

I have same problem too. Do you have fix it ?

Thx

[JohnMCMa]

It is caused by an outdated HUGO URL. I put a pull request (#25) on this.

[jounikuj]

More than a year has passed since this issue was opened and it appears that the outdated URL is still preventing the command hotspot3d uppro from running. @JohnMCMa made a pull request on this topic and presumably solved the issue. However, I am now getting the very same error message with his forked HotSpot3D version:

HotSpot3D::HugoGeneMethods::makeHugoGeneObjects ERROR: no data from url request. Installing Mozilla::CA might fix this issue.

Looks like the updated URL is also now outdated too. Because this issue significantly limits the usability of the HotSpot3D, I would be more than grateful if the authors would note this long-term problem and update the valid URLs to source code.

[danieljrichard]

I believe editing the file /home/user/perl5/lib/perl5/TGI/Mutpro/Preprocess/HugoGeneMethods.pm
may fix it?
I replaced this line:
#my $HugoUrl = "https://www.genenames.org/cgi-bin/hgnc_downloads?".
with this line
my $HugoUrl = "https://www.genenames.org/cgi-bin/download/custom?".

[Ansanqi]

I believe editing the file /home/user/perl5/lib/perl5/TGI/Mutpro/Preprocess/HugoGeneMethods.pm may fix it? I replaced this line: #my $HugoUrl = "https://www.genenames.org/cgi-bin/hgnc_downloads?". with this line my $HugoUrl = "https://www.genenames.org/cgi-bin/download/custom?".

Also not work.