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pcingola / SnpEff

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Download option a bit buggy #287

Closed marrip closed 3 years ago

marrip commented 3 years ago

Hey,

I am new to SnpEff and not sure what this is causing. I experience some problems when downloading a database via the download option. I am running:

java -jar snpEff.jar download GRCh38.99

The problem is I do not get any output, error messages or anything so I cannot really attach that here. It just starts and nothing really happens. I checked if any files were downloaded and found a new folder in data with the name of the database containing some bin files. But after a number of them were downloaded it kind of stops I think (as I said I do not get any kind of error or other output). I tried this on a Mac with openjdk 12.0.2 and SnpEff 5.0c. I also tried in a ubuntu docker container with openjdk 11.0.9.1 and the same version of SnpEff. Another thing I experienced was that the download did not even start when my workdir was not the unzipped snpeff directory. Is it only possible to download databases to the snpeff? If yes, maybe you could provide an option to download it to the workdir or an indicated path instead? I finally downloaded the database using wget - maybe this could be in the docs as well if it isn't yet?

Greetings from Sweden, Martin

pcingola commented 3 years ago

Try using the verbose command-line option -v to see more messages:

java -jar snpEff.jar download -v GRCh38.99

Also, I've updated the proxy capabilities in the latest version SnpEff 5.0d. If your network requires a proxy, then upgrading to this version might help.

If you have the ZIP database downloaded by wget, then it's just a matter of unzipping it to the right place. For instance in this case, the "*.bin" files should be snpEff/data/GRCh38.99 (assuming snpEff is the directory where you installed SnpEff and have the default data path in snpEff.config)

pcingola commented 3 years ago

Closing, feel free to reopen.