example-su92l-1kg.sh

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