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bioinfoUGR / sRNAtoolbox

small RNA analysis programs: standalone jar files (sRNAbench, sRNAde, etc), manuals and Docker image
MIT License
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Can't populate database #35

Open Enj0yce opened 2 months ago

Enj0yce commented 2 months ago

When trying to download the database (human miRBase) I use the populate command but it only tells me no species have been installed. Am I doing something wrong?

The command:

populate -db /opt/sRNAtoolboxDB

cris12gm commented 2 months ago

Dear @Enj0yce ,

In principle the command is ok, you can also type only populate. We just checked and there's no problem with the last version of the software downloading the last human genome (GRCh38_p13). Which version of the docker do you have? Have you tried using the last docker version available in dockerhub? https://hub.docker.com/layers/ugrbioinfo/srnatoolbox/0.0.6/images/sha256-84077aacaf13377b15c5efc00852df8242a00e9dab7f914581d4c8e3f11274b5?context=explore

Best, Cristina

Enj0yce commented 2 months ago

Hi @cris12gm ,

Thanks for your response. I am using Docker v4.33.1 and the latest version of sRNAtoolbox. Let me elaborate a little on the problem. When I try to trim and map my data I use the following command:

sRNAbench input=[path] output=[path] protocol=Q adapter=[sequence] umi=3pA12 species=GRCh38_p13_mp tRNA=GRCh38_p13_genomic_tRNA libs=GRCh38_p13_ncRNA libs=GRCh38_p13_RNAcentral tRNA=GRCh38_p13_genomic_tRNA libs=GRCh38_p13_cdna

I know the pre-processing works because when I run only that part of the command I have no problems.

When I run this I get the following message: The following bowtie indexes were not found /opt/sRNAtoolboxDB//index/GRCh38_p13_mp -- Will quite now!

Is there any way how I can pull/download the correct library files so this error doesn't occur anymore?