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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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file directories #27

Closed alantsangmb closed 5 years ago

alantsangmb commented 5 years ago

Hello, I have installed uvp via conda.

and I would like to ask where should I put the config.yml for pointing to the kraken database? I have looked into the /envs/reseqtb-uvp, but I can't find the "script" directory like the previous version.

And I have downloaded the SnpEff H37v data manually, where should I put this data directory? Thank you.

dfornika commented 5 years ago

Hi @alantsangmb, did you follow the installation instructions from the README.md?

https://github.com/CPTR-ReSeqTB/UVP#installation

If so, then you can edit the config file at uvp/config.yml.

https://github.com/CPTR-ReSeqTB/UVP/blob/master/uvp/config.yml

We have an update in the works (https://github.com/CPTR-ReSeqTB/UVP/pull/26) that will allow you to pass a config file from any location, or set those two parameters (krakendb and threads) directly on the command-line.

I'd recommend following the instructions for downloading the H37Rv snpEff database:

https://github.com/CPTR-ReSeqTB/UVP#download-the-m-tuberculosis-h37rv-snpeff-database

With your reseqtb-uvp conda environment active, run:

snpEff download m_tuberculosis_H37Rv

That will add the data to <your uvp env>/share/snpEff-<version>/data/m_tuberculosis_H37Rv/snpEffectPredictor.bin.

alantsangmb commented 5 years ago

Thank you so much. I thought the config file is located in the conda environment, but it is actually in the /uvp/ directory So UVP is now successfully installed via conda. And the config file is found in the /uvp/ directory and editable.

dfornika commented 5 years ago

@alantsangmb There is now a bioconda package for UVP v2.6.0. If you use that to install UVP, then the config file will be inside the environment in:

<your env>/lib/pythonX.Y/site-packages/uvp/config.yml

So if you install like this:

conda create -n uvp-2.6.0 uvp=2.6.0 python=3.6
conda activate uvp-2.6.0

...then the config file will be here:

miniconda3/envs/uvp-2.6.0/lib/python3.6/site-packages/uvp/config.yml

You'll still need to follow the GATK activation and snpEff download steps as described in the current installation instructions.

As I mentioned in the comment above, the next update (v2.7.0, if accepted) will allow you to use a -c or --config flag to pass a config file from any location.