example-su92l-1kg.sh

   1 #!/bin/bash
   2
   3 set -ex
   4
   5 PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
   6 go install
   7 lightning build-docker-image
   8 arv keep docker lightning-runtime
   9
  10 project=su92l-j7d0g-jzei0m9yvgauhjf
  11 gvcf=su92l-4zz18-bgyq36m6gctk63q
  12 info=su92l-4zz18-ykpcoea5nisz74f
  13 fasta=su92l-4zz18-s3e6as6uzsoocsb
  14 tags=su92l-4zz18-92bx4zjg5hgs3yc
  15
  16 unfiltered=$(
  17     lightning import       -project ${project} \
  18        -tag-library ${tags}/tagset.fa.gz \
  19        ${fasta})
  20 filtered=$(
  21     lightning filter       -project ${project} \
  22        -i ${unfiltered} \
  23        -min-coverage 0.9 -max-variants 30)
  24 numpy=$(
  25     lightning export-numpy -project ${project} \
  26        -i ${filtered})
  27 pca=$(
  28     lightning pca          -project ${project} \
  29        -i ${numpy})
  30 plot=$(
  31     lightning plot         -project ${project} \
  32        -i ${pca} \
  33        -labels-csv ${info}/sample_info.csv \
  34        -sample-fasta-dir ${fasta})
  35 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
  36 echo ${plot%%/*}