From 4227759ddbe61c69ef049cd3e607b4c345a04e2b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 15 Jan 2020 11:17:10 -0600
Subject: [PATCH] Add https_proxy in getBag process
---
workflow/conf/biohpc.config | 6 ++++++
workflow/rna-seq.nf | 1 +
2 files changed, 7 insertions(+)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index f71a85a..20da91a 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -20,4 +20,10 @@ process {
singularity {
enabled = true
cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+}
+
+env {
+ http_proxy = 'http://proxy.swmed.edu:3128'
+ https_proxy = 'http://proxy.swmed.edu:3128'
+ all_proxy = 'http://proxy.swmed.edu:3128'
}
\ No newline at end of file
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 0805296..c1d72ef 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -50,6 +50,7 @@ process getBag {
"""
hostname >>${repRID_getBag}.getBag.err
ulimit -a >>${repRID_getBag}.getBag.err
+ export https_proxy=\${http_proxy}
ln -sf `readlink -e credential.json` ~/.deriva/credential.json 2>>${repRID_getBag}.getBag.err
echo "LOG: deriva credentials linked" >>${repRID_getBag}.getBag.err
deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID_getBag} 2>>${repRID_getBag}.getBag.err
--
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