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genepi / haplogrep3

Free mtDNA Haplogroup Classification Service
https://haplogrep.i-med.ac.at/
MIT License
23 stars 2 forks source link

Incomplete installation documentation or release packaging error. #37

Closed vruano closed 1 month ago

vruano commented 7 months ago

Hi, recently I downloaded v3.2.1 for linux a and followed the simple instruction given in docs/installation.md.

However when executing haplogrep3 (without argument at least) it complains it cannot find tree.yaml. 

$ ./haplogrep3

Haplogrep 3 3.2.1                                                                                           
(c) 2022-2023 Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer                                                                                                     
Loading configuration from file 'haplogrep3.yaml' failed.                        
/..../haplogrep3-3.2.1/trees/phylotree-fu-rcrs/1.2/tree.yaml (No such file or directory) `

It turns out that there is another zip file ./trees/phylotree-fu-rcrs/1.2/package.zip that when unzipped at its parent directory produces the missing yaml together with other files that overwrite some files that are already "unzip".

I guess the best course of action would be remove the second unzip step and include every needed file directly in the main zip file.

seppinho commented 6 months ago

Hi, can you please try again with the latest version (v3.2.2) and see if the problem still persists?

Thanks! Sebastian

gqworks commented 2 months ago

I encountered the same error message, and was able to resolve it by running haplogrep with sudo. sudo ./haplogrep3

vruano commented 1 month ago

I encountered the same error message, and was able to resolve it by running haplogrep with sudo. sudo ./haplogrep3

That does not seem to follow best practices; sudo should not be necessary. I will retry with the latest myself and report here.

vruano commented 1 month ago

I can confirm that now using the latest seem to work for me v3.2.2 or at least I get to the point it shows the list of commands. Will close issue but @gqworks an any-other is welcome to reopen if they feel it needs to be.