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Commit 4227759d authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add https_proxy in getBag process

parent 33f96a38
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3 merge requests!37v0.0.1,!11Develop,!10Resolve "Add integration CI test"
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workflow/conf/biohpc.config
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...@@ -20,4 +20,10 @@ process { ...@@ -20,4 +20,10 @@ process {
singularity { singularity {
enabled = true enabled = true
cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/' 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
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View file @ 4227759d
...@@ -50,6 +50,7 @@ process getBag { ...@@ -50,6 +50,7 @@ process getBag {
""" """
hostname >>${repRID_getBag}.getBag.err hostname >>${repRID_getBag}.getBag.err
ulimit -a >>${repRID_getBag}.getBag.err ulimit -a >>${repRID_getBag}.getBag.err
export https_proxy=\${http_proxy}
ln -sf `readlink -e credential.json` ~/.deriva/credential.json 2>>${repRID_getBag}.getBag.err ln -sf `readlink -e credential.json` ~/.deriva/credential.json 2>>${repRID_getBag}.getBag.err
echo "LOG: deriva credentials linked" >>${repRID_getBag}.getBag.err echo "LOG: deriva credentials linked" >>${repRID_getBag}.getBag.err
deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID_getBag} 2>>${repRID_getBag}.getBag.err deriva-download-cli dev.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID_getBag} 2>>${repRID_getBag}.getBag.err
......
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