Script to remove genomes from the default galaxy-indices file

galaxy-delete_genomes.sh

# removing files from galaxyIndices that we don't need. 
# I'm going to create a very minimal version; no vertebrates

declare -a DELETE_GENOMES=(
  blastdb/htgs
  blastdb/wgs
  Amellifera_Honeybee
  Athaliana
  Btaurus
  Celegans/WS200
  Cfamiliaris_Dog
  Drerio_Zebrafish
  Ecaballus_Horse
  Fcatus_Cat
  Ggallus_Chicken
  Hsapiens
  microbes
  Mmulatta
  Mmusculus
  Msmegmatis
  Mtuberculosis_H37Rv
  Osjaponica
  Paeruginosa_UCBPP-PA14
  Rnorvegicus
  Spurpuratus
  Sscrofa
  Tguttata
  Xtropicalis
  Zmays
)

# remove files related to said genomes
for genome in ${DELETE_GENOMES[*]}
do
  rm -r /mnt/galaxyIndices/genomes/$genome
done
  

# remove unused liftover files. genomes may appear first or second, with the second version being upper case, hence the 2 versions for each line.

declare -a DELETE_LIFTOVER=(
  apiMel3 ApiMel3
  bosTau4 BosTau4 
  canFam2  CanFam2
  danRer5  DanRer5
  danRer6  DanRer6
  equCab2  EquCab2
  felCat3  FelCat3
  galGal3  GalGal3
  hg18  Hg18
  hg19  g19
  mm8  Mm8
  mm9  Mm9
  rheMac2  RheMac2
  rn4  Rn4
  strPur2  StrPur2
  susScr2  SusScr2
  taeGut1  TaeGut1
  xenTro2  XenTro2
)

for genome in ${DELETE_LIFTOVER[*]}
do
  find /mnt/galaxyIndices/liftOver/ -name "${genome}" -exec rm -f {} \;
done

# now remove unused program files... I will never use bowtie_color
find /mnt/galaxyIndices -name "bowtie_color" -exec rm -rf {} \;

# that should get us down to about 30GB?