search

AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
204 stars 25 forks source link

SSL certificate of the Pfam webpage has expired #28

Closed TlaskalV closed 4 years ago

TlaskalV commented 4 years ago

Hello Mike, when trying new conda installation of GToTree I was not able to finish gtt-test.sh command. It gives me downloading error for one of the models 

The problem child was PF00238.19.

When trying manual curl of the model, I got

curl: (60) SSL certificate problem: certificate has expired

It seems that referenced webpage can not be accessed. https://github.com/AstrobioMike/GToTree/blob/1ac6b35dfaf45ff81c288c12541049938b14bca8/bin/gtt-pfam-search#L368

Do you know how to heck the security settings of the curl? Maybe -k/--insecure option?

Thanks!

TlaskalV commented 4 years ago

Thanks for fast commit. Indeed, it expired yesterday according to my browser. Let's see if the Pfam support will renew it.

AstrobioMike commented 4 years ago

Beautiful :) Thanks so much for not only taking your time to tell me about this, but to also completely troubleshoot it!

The pfam certificate is out of date by 2 days, i'm sure they'll catch up with it soon, but can't really wait on it, so i've added the --insecure flag like you noted to the places where that is called (it happens in the main GToTree script and the gtt-pfam-search you pointed to depending on if it's called by itself with gtt-pfam-search or within a regular GToTree run – this is not sensible of course, just a consequence of me still being a messy, nascent "programmer", haha). Changes in https://github.com/AstrobioMike/GToTree/commit/7a307a87260d5a90c15707bfce32734540c47093

It's implemented in version 1.5.39, which is now updated and available through conda.

Thanks again so much for your time and info, @TlaskalV!