example-su92l-1kg.sh

   1 #!/bin/bash
   2
   3 set -ex
   4
   5 PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
   6 go install
   7 lightning build-docker-image
   8 arv keep docker lightning-runtime
   9
  10 priority=501
  11 project=su92l-j7d0g-jzei0m9yvgauhjf
  12 ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
  13 gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
  14 info=su92l-4zz18-ykpcoea5nisz74f
  15 tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
  16
  17 genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -ref ${ref_fa})
  18 fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})
  19 unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} ${fasta})
  20 filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")
  21 numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${filtered})
  22 pca=$(lightning        pca          -project ${project} -priority ${priority} -i ${numpy})
  23 plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
  24 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
  25 echo ${plot%%/*}