From 9fd3eb5acf3415dff74975ab5a7823624443f017 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 13 Feb 2021 11:56:40 -0600
Subject: [PATCH] Link deriva credentials for upload input/output bags
---
rna-seq.nf | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/rna-seq.nf b/rna-seq.nf
index 693199e..1fe526c 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -1335,6 +1335,12 @@ process uploadInputBag {
hostname > ${repRID}.uploadInputBag.log
ulimit -a >> ${repRID}.uploadInputBag.log
+ # link credential file for authentication
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.uploadInputBag.log
+ mkdir -p ~/.deriva
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo -e "LOG: linked" >> ${repRID}.uploadInputBag.log
+
yr=\$(date +'%Y')
mn=\$(date +'%m')
dy=\$(date +'%d')
@@ -2287,6 +2293,12 @@ process uploadOutputBag {
hostname > ${repRID}.uploadOutputBag.log
ulimit -a >> ${repRID}.uploadOutputBag.log
+ # link credential file for authentication
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.uploadOutputBag.log
+ mkdir -p ~/.deriva
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo -e "LOG: linked" >> ${repRID}.uploadOutputBag.log
+
yr=\$(date +'%Y')
mn=\$(date +'%m')
dy=\$(date +'%d')
--
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