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authorPjotr Prins2020-12-31 10:51:57 +0000
committerPjotr Prins2020-12-31 10:51:57 +0000
commitc54c6624ce864daec7640d938a98f196fde4ba1e (patch)
tree618047c0869630ffa2d86c4e4890e02266aa3173 /workflows/pull-data
parente33ce088225b9975a84a6724ab8e3a9f82964ec6 (diff)
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genbank: started on SPARQL fetcher
Diffstat (limited to 'workflows/pull-data')
-rw-r--r--workflows/pull-data/genbank/.guix-run11
-rwxr-xr-xworkflows/pull-data/genbank/genbank-fetch-ids3
-rwxr-xr-xworkflows/pull-data/genbank/genbank-fetch-ids.py0
3 files changed, 10 insertions, 4 deletions
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
--- a/workflows/pull-data/genbank/genbank-fetch-ids.py
+++ /dev/null