Export bed file.

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

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
old mode 100644 (file)
new mode 100755 (executable)
index 147585c..1e5ecbc
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -1,24 +1,27 @@
 #!/bin/bash
 
-go run . build-docker-image
+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
-gvcf=su92l-4zz18-ykpcoea5nisz74f
-fasta=su92l-4zz18-s3e6as6uzsoocsb
-tags=su92l-4zz18-92bx4zjg5hgs3yc
+ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
+gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
+info=su92l-4zz18-ykpcoea5nisz74f
+tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
 
-go run . import       -project ${project} \
-   -tag-library ~/keep/by_id/${tags}/tagset.fa.gz \
-   ~/keep/by_id/${fasta}
-go run . filter       -project ${project} \
-   -i ~/keep/by_id/su92l-4zz18-fcyucnod8y4515p/library.gob \
-   -min-coverage 0.9 -max-variants 30
-go run . export-numpy -project ${project} \
-   -i ~/keep/by_id/su92l-4zz18-l40xcd2l6dmphaj/library.gob
-go run . pca          -project ${project} \
-   -i ~/keep/by_id/su92l-4zz18-i6fzfoxpdh38yk4/library.npy
-go run . plot         -project ${project} \
-   -i ~/keep/by_id/su92l-4zz18-zqfo7qc3tadh6zb/pca.npy \
-   -labels-csv ~/keep/by_id/${gvcf}/sample_info.csv \
-   -sample-fasta-dir ~/keep/by_id/${fasta}
+genome=$(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 ${filtered} -one-hot)
+plot=$(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%%/*}