search

fbreitwieser / krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
GNU General Public License v3.0
223 stars 44 forks source link

dustmasker dependency #54

Open puethe opened 5 years ago

puethe commented 5 years ago

Hi, it seems that there's an implicit dependency on "dustmasker" for part of the functionality, but this isn't mentioned in the README and also doesn't get installed with install_krakenuniq.sh. This is particularly an issue when installing the software via conda. Would be great if this could be looked at! Many thanks in advance, Christoph

drpatelh commented 4 years ago

After fishing around the interwebnet it appears that the dustmasker executable is now a part of the BLAST+ suite of tools: https://github.com/tseemann/prokka/issues/256

Creating an environment.yml with the contents below provides dustmasker in the environment:

# You can use this file to create a conda environment:
#   conda env create -f environment.yml
name: krakenuniq-0.5.8
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - bioconda::krakenuniq=0.5.8
  - bioconda::blast=2.9.0