From 347b8dce36832c6d3e379d81b3efefcbc88a3117 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 30 Apr 2020 10:22:27 -0400
Subject: Wrap import script to run as a workflow

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 scripts/import_to_arvados.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 scripts/import_to_arvados.py

(limited to 'scripts/import_to_arvados.py')

diff --git a/scripts/import_to_arvados.py b/scripts/import_to_arvados.py
new file mode 100644
index 0000000..07b7d71
--- /dev/null
+++ b/scripts/import_to_arvados.py
@@ -0,0 +1,13 @@
+import os
+import subprocess
+import glob
+import sys
+
+os.chdir(os.environ["TMPDIR"])
+subprocess.run(sys.argv[1])
+
+os.chdir("fasta_and_yaml")
+fasta_files = glob.glob("*.fasta")
+
+for f in fasta_files:
+    subprocess.run(["bh20-seq-uploader", f, "%s.yaml" %f[:-6]])
-- 
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