I/O pipeline, show arvados container logs.

[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..7bd631b
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -1,6 +1,10 @@
 #!/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
 
 project=su92l-j7d0g-jzei0m9yvgauhjf
@@ -8,17 +12,25 @@ gvcf=su92l-4zz18-ykpcoea5nisz74f
 fasta=su92l-4zz18-s3e6as6uzsoocsb
 tags=su92l-4zz18-92bx4zjg5hgs3yc
 
-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/${fasta}
+unfiltered=$(
+    lightning import       -project ${project} \
+       -tag-library ${tags}/tagset.fa.gz \
+       ${fasta})
+unfiltered=su92l-4zz18-fcyucnod8y4515p/library.gob
+filtered=$(
+    lightning filter       -project ${project} \
+       -i ${unfiltered} \
+       -min-coverage 0.9 -max-variants 30)
+numpy=$(
+    lightning export-numpy -project ${project} \
+       -i ${filtered})
+pca=$(
+    lightning pca          -project ${project} \
+       -i ${numpy})
+plot=$(
+    lightning plot         -project ${project} \
+       -i ${pca} \
+       -labels-csv ${gvcf}/sample_info.csv \
+       -sample-fasta-dir ${fasta})
+echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
+echo ${plot%%/*}