Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

url? #23

Open
YonkoBigMom opened this issue Feb 3, 2019 · 5 comments
Open

url? #23

YonkoBigMom opened this issue Feb 3, 2019 · 5 comments

Comments

@YonkoBigMom
Copy link

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
Copy link

hi, YonkoBigMom.

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

Thx

@JohnMCMa
Copy link

It is caused by an outdated HUGO URL.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

@jounikuj
Copy link

More than a year has passed since this issue was opened and it appears that the outdated URL is still preventing the command hotspot3d uppro from running.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Looks like the updated URL is also now outdated too.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
Copy link

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
Copy link

Ansanqi commented Aug 29, 2023

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

6 participants