search

bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
19 stars 9 forks source link

Run ktUpdateTaxonomy.sh after installing matam conda environment ? #101

Closed ppericard closed 4 years ago

ppericard commented 4 years ago

After install the matam conda environment, we have a warning message. Do we need to run ktUpdateTaxonomy.sh ?

Executing transaction: - b'\nKrona installed.  You still need to manually update the taxonomy\ndatabases before Krona can generate taxonomic reports.  The update\nscript is ktUpdateTaxonomy.sh.  The default location for storing\ntaxonomic databases is /home/ubuntu/miniconda3/envs/matam/opt/krona/taxonomy\n\nIf you would like the taxonomic data stored elsewhere, simply replace\nthis directory with a symlink.  For example:\n\nrm -rf /home/ubuntu/miniconda3/envs/matam/opt/krona/taxonomy\nmkdir /path/on/big/disk/taxonomy\nln -s /path/on/big/disk/taxonomy /home/ubuntu/miniconda3/envs/matam/opt/krona/taxonomy\nktUpdateTaxonomy.sh\n\n'                               | b'The default QUAST package does not include:\n* GRIDSS (needed for structural variants detection)\n* SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets)\n* BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only!\n\nTo be able to use those, please run\n    quast-download-gridss\n    quast-download-silva\n    quast-download-busco\n'
loic-couderc commented 4 years ago

From krona, we use "ktImportText". This tools is not concern by the "ktUpdateTaxonomy" script. So we do not need to run it.

ppericard commented 4 years ago

ok