diff --git a/db-scripts/build-plasmids-db-plsdb.sh b/db-scripts/build-plasmids-db-plsdb.sh index 060224c..1d6fd5d 100644 --- a/db-scripts/build-plasmids-db-plsdb.sh +++ b/db-scripts/build-plasmids-db-plsdb.sh @@ -1,15 +1,14 @@ echo "Download plasmid sequences..." -wget -O plasmids-plsdb.zip https://ccb-microbe.cs.uni-saarland.de/plsdb/plasmids/download/?zip +wget -O plasmids-plsdb.bz2 https://ccb-microbe.cs.uni-saarland.de/plsdb/plasmids/download/plsdb.fna.bz2 echo "Unzip plasmid sequences..." -unzip plasmids-plsdb.zip -blastdbcmd -entry all -db plsdb.fna -out plsdb.fna +bunzip2 plsdb.fna.bz2 nextflow run $REFERENCE_SEEKER_HOME/db-scripts/build-plasmids-db-plsdb.nf --plasmids plsdb.fna || { echo "Nextflow failed!"; exit; } mash paste db sketches/*.msh || { echo "Mash failed!"; exit; } -rm -rf work/ .nextflow* sketches/ plsdb* README.md +rm -rf work/ .nextflow* sketches/ plsdb.fna mv db.msh plasmids-plsdb/