shiny_db:
  db_path: ~/.BioInstaller/BioInstaller.shiny.sqlite
  db_type: sqlite
shiny_db_table:
  output_file_table_name: output_files
  task_table_admin_key: BioInstaller_admin
  task_table_name: task_info
  upload_data_table_colnames:
  - file_name
  - file_path
  - file_size
  - file_type
  - genome_version
  - upload_time
  - md5
  - description
  upload_data_table_name: upload_data
  user_table_name: users
  user_talbe_colnames:
  - uid
  - username
  - password
shiny_plugins:
  shiny_plugin_dir: ~/.BioInstaller/plugins
shiny_download:
  download_dir: ~/.BioInstaller/download
shiny_output:
  out_dir: ~/.BioInstaller/output
  tmp_dir: ~/.BioInstaller/tmp
shiny_preview:
  fread:
  - csv
  - txt
  - avinput
  browser:
  - pdf
  - png
  - jpg
  - jpeg
  - zip
shiny_queue:
  log_dir: ~/.BioInstaller/log
  name: BioInstaller_shiny
  queue_db: ~/.BioInstaller/BioInstaller.shiny.queue.sqlite
shiny_tools:
  pipeline: easy_project
  instant:
      - bioinstaller
      - spack
      - conda
      - datasets2tools
      - pubmed 
      - geoquery
      - maftools
shiny_tools_params:
    require:
      bioinstaller: BioInstaller
      conda: BioInstaller
      spack: BioInstaller
      datasets2tools:
          - RCurl
          - jsonlite
      pubmed:
          - rentrez
          - XML
      geoquery: GEOquery
      maftools: maftools
shiny_upload:
  upload_dir: ~/.BioInstaller/upload
  supported_genome_version:
  - hg19
  - hg38
  - mm10
  - mm9
  supported_file_type:
  - auto
  - ab1
  - acedb
  - affybatch
  - afg
  - arff
  - asn1
  - avinput
  - avinput.gz
  - axt
  - bai
  - bam
  - bcf
  - bed
  - bed12
  - bed6
  - bedgraph
  - bedstrict
  - bgzip
  - bif
  - bigbed
  - bigwig
  - biom1
  - blastdbd
  - blastdbn
  - blastdbp
  - blastxml
  - bmp
  - btf
  - btwisted
  - cai
  - cel
  - charge
  - checktrans
  - chips
  - chrint
  - cisml
  - clustal
  - cml
  - codata
  - codcmp
  - coderet
  - compseq
  - consensusxml
  - cpgplot
  - cpgreport
  - cps
  - cram
  - csfasta
  - csv
  - csv.gz
  - ct
  - cusp
  - customtrack
  - cut
  - cxb
  - dan
  - data
  - dbmotif
  - dbn
  - diffseq
  - digest
  - dmnd
  - dreg
  - eigenstratgeno
  - eigenstratpca
  - einverted
  - eland
  - elandmulti
  - embl
  - encodepeak
  - epestfind
  - eps
  - equicktandem
  - eset
  - est2genome
  - etandem
  - excel
  - fai
  - fasta
  - fastq
  - fastq.gz
  - fastqcssanger
  - fastqillumina
  - fastqsanger
  - fastqsolexa
  - feattable
  - featurexml
  - fitch
  - fli
  - fped
  - fphe
  - fps
  - fqtoc
  - freak
  - fuzznuc
  - fuzzpro
  - fuzztran
  - garnier
  - gcg
  - geecee
  - genbank
  - genetrack
  - gff
  - gff3
  - gg
  - gif
  - gtf
  - gz
  - h5
  - hardklor
  - hdt
  - helixturnhelix
  - hennig86
  - hlf
  - hmm2
  - hmm3
  - hmoment
  - html
  - idpdb
  - idxml
  - ig
  - im
  - inchi
  - interval
  - ipynb
  - isochore
  - jackknifer
  - jackknifernon
  - jpg
  - json
  - jsonld
  - kronik
  - laj
  - lav
  - ldindep
  - len
  - linecount
  - lped
  - maf
  - maf.gz
  - mafcustomtrack
  - malist
  - markx0
  - markx1
  - markx10
  - markx2
  - markx3
  - mascotdat
  - match
  - mega
  - meganon
  - memexml
  - mgf
  - mol
  - mol2
  - motif
  - mrxs
  - ms2
  - msp
  - mzdata
  - mzid
  - mzml
  - mzq
  - mzxml
  - n3
  - nametable
  - ncbi
  - ndpi
  - needle
  - neostore
  - netcdf
  - newcpgreport
  - newcpgseek
  - nex
  - nexus
  - nexusnon
  - nhdr
  - nhx
  - noreturn
  - nrrd
  - nt
  - obfs
  - obo
  - owl
  - oxlicg
  - oxligl
  - oxling
  - oxliss
  - oxlist
  - oxlits
  - pair
  - palindrome
  - pbed
  - pbm
  - pcd
  - pcx
  - pdb
  - pdf
  - pepcoil
  - pepinfo
  - pepstats
  - pepxml
  - percin
  - percout
  - pgm
  - phar
  - pheno
  - phylip
  - phylipnon
  - phyloxml
  - pileup
  - pir
  - plyascii
  - plybinary
  - png
  - polydot
  - pphe
  - ppm
  - preg
  - prettyseq
  - primersearch
  - protxml
  - psd
  - ptalign
  - ptalignca
  - ptalignfiltered
  - ptalignfilteredca
  - ptaligntrimmed
  - ptaligntrimmedca
  - ptortho
  - ptorthocs
  - ptphylip
  - pttgf
  - pttree
  - qcml
  - qual
  - qual454
  - qualillumina
  - qualsolexa
  - qualsolid
  - rast
  - rdata
  - rdf
  - regions
  - rexpbase
  - rgb
  - rgenetics
  - sam
  - scf
  - scidx
  - scn
  - score
  - sdf
  - seqtable
  - sf3
  - sff
  - showfeat
  - showorf
  - sif
  - simple
  - sixpack
  - smat
  - smi
  - snpeffdb
  - snpmatrix
  - snpsiftdbnsfp
  - snptest
  - splib
  - sqlite
  - sra
  - srs
  - srspair
  - staden
  - stl
  - stockholm
  - strider
  - supermatcher
  - svg
  - svs
  - svslide
  - swiss
  - syco
  - tabix
  - table
  - tabular
  - tagseq
  - tandem
  - tar
  - taxonomy
  - textsearch
  - tf2
  - tf8
  - tif
  - tiff
  - trackhub
  - trafoxml
  - traml
  - triples
  - tsv
  - ttl
  - twobit
  - txt
  - txt.gz
  - uniprotxml
  - vcf
  - vcf.gz
  - vectorstrip
  - velvet
  - vms
  - vmu
  - vtkascii
  - vtkbinary
  - wiff
  - wig
  - wobble
  - wordcount
  - xbm
  - xgmml
  - xls
  - xlsx
  - xmfa
  - xml
  - xpm
  - zip
