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Russel88 / CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
https://typer.crispr.dk
MIT License
89 stars 16 forks source link

No database with conda install? #29

Closed nicholascdove closed 2 years ago

nicholascdove commented 2 years ago

Hello, I installed cctyper with conda, conda create -n cctyper -c conda-forge -c bioconda -c russel88 cctyper activated the environment, conda activate cctyper and then tried to run cctyper cctyper ~/Downloads/44_contigs_1000.fasta ~/Desktop/cctyper_output_44 --prodigal meta

However, it says that it cannot find the database directory. Is there an easy way to fix this?

[2022-08-03 13:40:32] INFO: Running CRISPRCasTyper version 1.3.0 [2022-08-03 13:40:32] ERROR: Could not find database directory

Thanks,

Nicholas

Russel88 commented 2 years ago

Hi Nicholas,

The quick fix is the set the CCTYPER_DB shell variable to the path where the database is located. This should normally happen automatically, though. export CCTYPER_DB="/path/to/conda/envs/cctyper/db

If the database isn't downloaded, for some reason, you can see here how to downlaod it manually: https://github.com/Russel88/CRISPRCasTyper#when-installing-with-pip-you-need-to-download-the-database-manually

By the way, I can see you are using an old version of CCTyper. It might also help to recreate the conda env with the newest version (1.6.4).

Cheers, Jakob

nicholascdove commented 2 years ago

The quick fix did it! Thanks!