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OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
22 stars 8 forks source link

confindr_database_setup #43

Closed joergFLI closed 1 year ago

joergFLI commented 1 year ago

Dear ConFindR-Team,

after successfull installation using conda and successfully running your example data, I fail in downloading the rmlst data. My problem is that the script confindr_database_setup is not included within conda3/envs/confindr/bin/

Any idea?

evezeyl commented 1 year ago

database_setup_modified.zip Hi, I am reinstalling myself - Last time I had to modify a bit the setup script (if I remember well it was just a minor modification). I am reusing that and it worked.

Some of the schemes are under licence, eg rmlst scheme you will need to ask for a licence in pubMLST, during the setup it will ask you to connect to to pubMLST and authorize the access of confindr to the scheme. Hope this helps. All the best. Eve

pcrxn commented 1 year ago

Hi @joergFLI, could you please try installing the latest version of ConFindr into a new Conda envirionment by running conda create -n confindr -c bioconda confindr=0.7.4?

confindr_database_setup should be located within the Conda environment's bin/ directory, so I'm not sure why it wouldn't be appearing for you there, unless an older version of ConFindr was installed by Conda, perhaps?

pcrxn commented 1 year ago

I'll close this in a couple of weeks if there's no more activity.

pcrxn commented 1 year ago

Closing since no further updates since Nov 4.