From c54c6624ce864daec7640d938a98f196fde4ba1e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 31 Dec 2020 10:51:57 +0000
Subject: genbank: started on SPARQL fetcher

---
 workflows/pull-data/genbank/.guix-run            | 11 +++++++----
 workflows/pull-data/genbank/genbank-fetch-ids    |  3 +++
 workflows/pull-data/genbank/genbank-fetch-ids.py |  0
 3 files changed, 10 insertions(+), 4 deletions(-)
 create mode 100755 workflows/pull-data/genbank/genbank-fetch-ids
 delete mode 100755 workflows/pull-data/genbank/genbank-fetch-ids.py

(limited to 'workflows/pull-data')

diff --git a/workflows/pull-data/genbank/.guix-run b/workflows/pull-data/genbank/.guix-run
index 1403c69..6db7871 100644
--- a/workflows/pull-data/genbank/.guix-run
+++ b/workflows/pull-data/genbank/.guix-run
@@ -1,5 +1,8 @@
-#!/bin/sh
-# Runner
+# Set up the Guix environment with dependencies
+#
+
+echo # next run:
+echo 'export PATH=$GUIX_ENVIRONMENT/bin:$PATH'
+
+~/.config/guix/current/bin/guix environment guix --ad-hoc python python-biopython python-requests python-dateutil ruby
 
-echo python3 from_genbank_to_fasta_and_yaml.py
-guix environment guix --ad-hoc python python-biopython python-requests python-dateutil
diff --git a/workflows/pull-data/genbank/genbank-fetch-ids b/workflows/pull-data/genbank/genbank-fetch-ids
new file mode 100755
index 0000000..00f693f
--- /dev/null
+++ b/workflows/pull-data/genbank/genbank-fetch-ids
@@ -0,0 +1,3 @@
+#!/usr/bin/env ruby
+#
+#
diff --git a/workflows/pull-data/genbank/genbank-fetch-ids.py b/workflows/pull-data/genbank/genbank-fetch-ids.py
deleted file mode 100755
index e69de29..0000000
-- 
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