Add https_proxy in getBag process

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

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