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author | Peter Amstutz | 2020-04-30 10:22:27 -0400 |
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committer | Peter Amstutz | 2020-04-30 10:22:27 -0400 |
commit | 347b8dce36832c6d3e379d81b3efefcbc88a3117 (patch) | |
tree | 1d0f62247576dfd746511aed683acd65072b1783 /scripts/import_to_arvados.py | |
parent | 3475c3e30197a11ada10d1b0a4bafb026f2fb580 (diff) | |
download | bh20-seq-resource-347b8dce36832c6d3e379d81b3efefcbc88a3117.tar.gz bh20-seq-resource-347b8dce36832c6d3e379d81b3efefcbc88a3117.tar.lz bh20-seq-resource-347b8dce36832c6d3e379d81b3efefcbc88a3117.zip |
Wrap import script to run as a workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'scripts/import_to_arvados.py')
-rw-r--r-- | scripts/import_to_arvados.py | 13 |
1 files changed, 13 insertions, 0 deletions
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]]) |