example-su92l-1kg.sh

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