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ngless-toolkit / ngless

NGLess: NGS with less work
https://ngless.embl.de
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Reference genomes not available Mus musculus #106

Closed kunstner closed 5 years ago

kunstner commented 5 years ago

Hi,

I'm testing ngless version 1.0 (and 0.6.x) for a metagenomics project. Unfortunately, I do not manage to download the reference for Mus musculus; neither mm10.p5 nor mm10.p2 or working. I've tested two different environments (HPC and Virtual Machine) but the results are similar.

` NGLESS=~/tmp/ngless-1.0.0/bin/ngless $NGLESS --install-reference-data mm10.p5 [Fri 10-05-2019 10:11]: Starting download from https://ngless.embl.de/resources/References/mm10.p5.tar.gz Exiting after fatal error while installing data System Error Could not connect to https://ngless.embl.de/resources/References/mm10.p5.tar.gz (got error code: 404)

`

Other references than mm10 or working (e.g. ce10).

Any advice on how to fix this problem?

Best, Axel

unode commented 5 years ago

Hi Axel,

This is an issue on our side, paths pointing to the incorrect location. We'll fix it and let you know as soon as possible.

Sorry for the inconvenience.

kunstner commented 5 years ago

Hi @unode, thanks for the fast response! Axel

unode commented 5 years ago

There's also a versioning issue affecting --install-reference-data. Since there's no ngless script/directive it defaults to NGLVersion 0 0 as per: https://github.com/ngless-toolkit/ngless/blob/8bd5681a7b75c3be9ea46dae8c9b2bbf67928ae3/NGLess/NGLess/NGLEnvironment.hs#L42

I think the saner option would be to require specifying the version:

ngless --install-reference-data 1.0 mm10.p5

which would in turn allow matching the different versions. @luispedro your thoughts?

luispedro commented 5 years ago

The immediate issue is fixed, @kunstner please try again

The issue of no-versioning is a trickier one. Given that we have 1.0 out, we will probably not update for a bit (unlike in the run up to 1.0, where we had a release every couple of months, it seems), so it's not that urgent. But so far, we have not changed the actual references, I believe, so the issue is not that big of a deal.

kunstner commented 5 years ago

The immediate issue is fixed, @kunstner please try again

Thanks @luispedro for the quick fix. Seems to be working now. Best

unode commented 5 years ago

As the original issue is fixed I'm marking it as closed. The issue of no versioning is now in #107 .