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140 lines (111 loc) · 4.86 KB
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#! /bin/bash
rroot=$(git rev-parse --show-toplevel)
### NCBI_rep_genomes #####################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/NCBI_rep_genomes
for build in NCBI_rep_genomes/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
# Link to the latest
cd /lustre/groups/cbi/shared/Databases/NCBI_rep_genomes && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### NCBI_16SMicrobial ####################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/NCBI_16SMicrobial
for build in NCBI_16SMicrobial/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/NCBI_16SMicrobial && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### NCBI_rep_protozoa ####################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/NCBI_rep_protozoa
for build in NCBI_rep_protozoa/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/NCBI_rep_protozoa && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### NCBI_rep_fungi #######################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/NCBI_rep_fungi
for build in NCBI_rep_fungi/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/NCBI_rep_fungi && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### wormbase_parasite #######################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/wormbase_parasite
for build in wormbase_parasite/????????; do
rsync -av $build/*.bt2* /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/wormbase_parasite && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### Human Microbiome Prroject ###############################################################
mkdir -p /lustre/groups/cbi/shared/Databases/HMP
for build in HMP/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/HMP && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### plasmaDB #############################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/plasmaDB
for build in plasmaDB/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/plasmaDB && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### cfDB #################################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/cfDB
for build in cfDB/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/cfDB && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### kraken database ######################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/kraken
for build in kraken/????????; do
rsync -av $build/* /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/kraken && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### centrifuge database ##################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/centrifuge
for build in centrifuge/????????; do
rsync -av $build/*.cf /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/centrifuge && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### plant marker database ################################################################
mkdir -p /lustre/groups/cbi/shared/Databases/plant_markers
for build in plant_markers/????????; do
rsync -av $build/*.bt2 /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/plant_markers && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot
### centrifuge_NCBI database #############################################################
mkdir -p /lustre/groups/cbi/shared/Databases/centrifuge_NCBI
for build in centrifuge_NCBI/????????; do
rsync -av $build/centrifuge_*/????????/*.cf /lustre/groups/cbi/shared/Databases/$build
done
cd /lustre/groups/cbi/shared/Databases/centrifuge_NCBI && \
rm -f latest && \
ln -s $(ls . | sort | tail -n1) latest && \
cd $rroot