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View Code? Open in Web Editor NEWA Dockerfile and wrappers for the Kraken metagenomic classifier
A Dockerfile and wrappers for the Kraken metagenomic classifier
Use the scripts at this webpage
which basically consists of:
# clone the git repo
git clone https://github.com/mw55309/Kraken_db_install_scripts.git
# either put the scripts in your path or run them from that directory
# make download directory
mkdir downloads
cd downloads
# run for each branch of life you wish to download
perl download_bacteria.pl
perl download_archaea.pl
perl download_fungi.pl
perl download_protozoa.pl
perl download_viral.pl
# you should now have five directories, one for each branch
# build a new database
# download taxonomy
kraken-build --download-taxonomy --db kraken_bvfpa_080416
# for each branch, add all fna in the directory to the database
for dir in fungi protozoa archaea viral bacteria; do
for fna in `ls $dir/*.fna`; do
kraken-build --add-to-library $fna --db kraken_bvfpa_080416
done
done
# build the actual database
kraken-build --build --db kraken_bvfpa_080416
Forked it in case it goes away
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