From 7fabc4f9427856600e237c6cacd710f49b88d45d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 24 Aug 2020 10:31:24 +0100
Subject: Genbank upload

---
 doc/blog/using-covid-19-pubseq-part3.org | 12 ++++++++++++
 1 file changed, 12 insertions(+)

(limited to 'doc/blog/using-covid-19-pubseq-part3.org')

diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index b1ab90d..fda7be8 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -236,3 +236,15 @@ The web interface using this exact same script so it should just work
 We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA
 and YAML]] extractor specific for GenBank. This means that the steps we
 took above for uploading a GenBank sequence are already automated.
+
+The steps are: from the
+~bh20-seq-resource/scripts/download_genbank_data/~ directory
+
+#+BEGIN_SRC sh
+python3 from_genbank_to_fasta_and_yaml.py
+dir_fasta_and_yaml=~/bh20-seq-resource/scripts/download_genbank_data/fasta_and_yaml
+ls $dir_fasta_and_yaml/*.yaml | while read path_code_yaml; do
+   path_code_fasta=${path_code_yaml%.*}.fasta
+   bh20-seq-uploader --skip-qc $path_code_yaml $path_code_fasta
+done
+#+END_SRC
-- 
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