Update example.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index 1e5ecbc1b348535695714d096c7e88c173202c24..f8701b22b9ebd7de84cf507fd3bb37d26c66f815 100755 (executable)
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -10,18 +10,36 @@ arv keep docker lightning-runtime
 priority=501
 project=su92l-j7d0g-jzei0m9yvgauhjf
 ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
+ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
 gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
 info=su92l-4zz18-ykpcoea5nisz74f
 tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
 
-genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -ref ${ref_fa})
-fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})
-unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true ${fasta})
-stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${unfiltered})
-filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")
-#numpy=$(lightning     export-numpy -project ${project} -priority ${priority} -i ${filtered} -one-hot)
-#pca=$(lightning       pca-py       -project ${project} -priority ${priority} -i ${numpy})
-pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${filtered} -one-hot)
+genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -ref ${ref_fa})                                                          ; echo genome=${genome}
+fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})                     ; echo fasta=${fasta}
+# fasta=su92l-4zz18-9nq05jifgz7iult
+
+ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
+# ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
+# 539s
+
+unfiltered=$(lightning import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta})       ; echo unfiltered=${unfiltered}
+# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
+
+merged=$(lightning     merge        -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib})                                              ; echo merged=${merged}
+# merged=su92l-4zz18-bfs0wc658kbf3lf/library.gob
+# 2400s
+
+exportvcf=$(lightning  export       -project ${project} -priority ${priority} -i ${merged} -output-format vcf -ref /mnt/su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz -output-bed export.bed) ; echo exportvcf=${exportvcf}
+# exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
+# 5506s
+
+stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${unfiltered})                                                        ; echo stats=${stats}
+filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")                 ; echo filtered=${filtered}
+
+pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${filtered} -one-hot)                                                 ; echo pca=${pca}
 plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
 echo ${plot%%/*}
+
+numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${filtered} -one-hot)