example-su92l-1kg.sh

   1 #!/bin/bash
   2
   3 set -ex
   4
   5 PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
   6 go install
   7 lightning build-docker-image
   8 arv keep docker lightning-runtime
   9
  10 priority=501
  11 project=su92l-j7d0g-jzei0m9yvgauhjf
  12 ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
  13 ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
  14 gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
  15 info=su92l-4zz18-ykpcoea5nisz74f
  16 tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
  17
  18 genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -ref ${ref_fa})                                                          ; echo genome=${genome}
  19 fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})                     ; echo fasta=${fasta}
  20 # fasta=su92l-4zz18-9nq05jifgz7iult
  21
  22 ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
  23 # ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
  24 # 539s
  25
  26 ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref_fa}) ; echo ref38_lib=${ref38_lib}
  27 # ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
  28
  29 unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta})       ; echo unfiltered=${unfiltered}
  30 # unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
  31
  32 merged=$(lightning     merge        -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib})                                              ; echo merged=${merged}
  33 # merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
  34 # 2400s
  35
  36 exportvcf=$(lightning  export       -project ${project} -priority ${priority} -i ${merged} -output-format vcf -ref /mnt/su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz -output-bed export.bed) ; echo exportvcf=${exportvcf}
  37 # exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
  38 # 5506s
  39
  40 stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${merged})                                                            ; echo stats=${stats}
  41
  42 filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30")                     ; echo filtered=${filtered}
  43
  44 annotations=$(lightning annotate    -project ${project} -priority ${priority} -i ${merged})                                                            ; echo annotations=${annotations}
  45
  46 pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${filtered} -one-hot)                                                 ; echo pca=${pca}
  47 plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
  48 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
  49 echo ${plot%%/*}
  50
  51
  52 merged38=$(lightning   merge        -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib})                                              ; echo merged38=${merged38}
  53 # merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
  54 # 1602s
  55
  56 numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${merged38} -max-variants "30" -min-coverage "0.9")                   ; echo numpy=${numpy}
  57 # numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
  58 # 6155s
  59 # pcapy=$(lightning      pca          -project ${project} -priority ${priority} -i ${numpy})                                                             ; echo pcapy=${pcapy}
  60 comvar=$(lightning     numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv)           ; echo comvar=${comvar}