From f355c46181c2cd76f904aece314c7e8f59ad084d Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 18 Feb 2021 11:59:24 -0600
Subject: [PATCH] Fix missing auth file processes
---
rna-seq.nf | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/rna-seq.nf b/rna-seq.nf
index 7698d47..59f2039 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -1418,6 +1418,12 @@ process uploadExecutionRun {
hostname > ${repRID}.uploadExecutionRun.log
ulimit -a >> ${repRID}.uploadExecutionRun.log
+ # link credential file for authentication
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.uploadExecutionRun.log
+ mkdir -p ~/.deriva
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo -e "LOG: linked" >> ${repRID}.uploadExecutionRun.log
+
echo LOG: searching for workflow RID - BICF mRNA ${workflow.manifest.version} >> ${repRID}.uploadExecutionRun.log
workflow=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Workflow/Name=BICF%20mRNA%20Replicate/Version=${workflow.manifest.version})
workflow=\$(echo \${workflow} | grep -o '\\"RID\\":\\".*\\",\\"RCT')
@@ -2127,6 +2133,12 @@ process uploadQC {
hostname > ${repRID}.uploadQC.log
ulimit -a >> ${repRID}.uploadQC.log
+ # link credential file for authentication
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.uploadQC.log
+ mkdir -p ~/.deriva
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo -e "LOG: linked" >> ${repRID}.uploadQC.log
+
if [ "${ends}" == "pe" ]
then
end="Paired End"
@@ -2623,6 +2635,12 @@ process uploadQC_fail {
hostname > ${repRID}.uploadQC.log
ulimit -a >> ${repRID}.uploadQC.log
+ # link credential file for authentication
+ echo -e "LOG: linking deriva credentials" >> ${repRID}.uploadQC.log
+ mkdir -p ~/.deriva
+ ln -sf `readlink -e credential.json` ~/.deriva/credential.json
+ echo -e "LOG: linked" >> ${repRID}.uploadQC.log
+
cookie=\$(cat credential.json | grep -A 1 '\\"${source}\\": {' | grep -o '\\"cookie\\": \\".*\\"')
cookie=\${cookie:11:-1}
--
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