5 PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
7 lightning build-docker-image
8 arv keep docker lightning-runtime
10 project=su92l-j7d0g-jzei0m9yvgauhjf
11 gvcf=su92l-4zz18-ykpcoea5nisz74f
12 fasta=su92l-4zz18-s3e6as6uzsoocsb
13 tags=su92l-4zz18-92bx4zjg5hgs3yc
16 lightning import -project ${project} \
17 -tag-library ${tags}/tagset.fa.gz \
19 unfiltered=su92l-4zz18-fcyucnod8y4515p/library.gob
21 lightning filter -project ${project} \
23 -min-coverage 0.9 -max-variants 30)
25 lightning export-numpy -project ${project} \
28 lightning pca -project ${project} \
31 lightning plot -project ${project} \
33 -labels-csv ${gvcf}/sample_info.csv \
34 -sample-fasta-dir ${fasta})
35 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"