Merge branch '21543-lightning-subdir'

[lightning.git] / example-su92l-1kg.sh

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
deleted file mode 100755 (executable)
index 4e60823..0000000
--- a/example-su92l-1kg.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/bash
-
-set -ex
-
-PATH="${GOPATH:-${HOME}/go}/bin:${PATH}"
-go install
-lightning build-docker-image
-arv keep docker lightning-runtime
-
-priority=501
-project=su92l-j7d0g-jzei0m9yvgauhjf
-ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
-ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
-gvcf=${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 ${ref_fa})                                                          ; echo genome=${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-svw5xqe5g0ct2v1/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 ${merged})                                                            ; echo stats=${stats}
-
-filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30")                     ; echo filtered=${filtered}
-
-annotations=$(lightning annotate    -project ${project} -priority ${priority} -i ${merged})                                                            ; echo annotated=${annotated}
-
-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)