diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config index f71a85a849add641abf42a95986ed12865c63de6..20da91a7f7a241e610708d7186d299d397958c41 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 08052962f4e07a2115745aaaa5f5679b6c3fa1e4..c1d72efac168ca372471a35e4baa9ccfd96aae18 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