From 785c48585f34224c4df2d8a19719891c692ef38f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 12 Feb 2021 22:33:42 -0600
Subject: [PATCH] Change bdbag to use cookie locally
---
conf/bdbag.json | 28 ++++++++++++++++++++++++++++
rna-seq.nf | 12 +++++++-----
workflow/scripts/bdbag_fetch.sh | 4 ++--
3 files changed, 37 insertions(+), 7 deletions(-)
create mode 100644 conf/bdbag.json
diff --git a/conf/bdbag.json b/conf/bdbag.json
new file mode 100644
index 0000000..2c2ab24
--- /dev/null
+++ b/conf/bdbag.json
@@ -0,0 +1,28 @@
+{
+ "fetch_config": {
+ "http": {
+ "http_cookies": {
+ "file_names": [
+ "*cookies.txt"
+ ],
+ "scan_for_cookie_files": true,
+ "search_paths": [
+ "."
+ ],
+ "search_paths_filter": "*cookies.txt"
+ }
+ },
+ "https": {
+ "http_cookies": {
+ "file_names": [
+ "*cookies.txt"
+ ],
+ "scan_for_cookie_files": true,
+ "search_paths": [
+ "."
+ ],
+ "search_paths_filter": "*cookies.txt"
+ }
+ }
+ }
+}
diff --git a/rna-seq.nf b/rna-seq.nf
index 763581a..5b15367 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -72,6 +72,7 @@ spikeForce = params.spikeForce
email = params.email
// Define fixed files and variables
+bdbagConfig = Channel.fromPath("${baseDir}/conf/bdbag.json")
replicateExportConfig = Channel.fromPath("${baseDir}/conf/Replicate_For_Input_Bag.json")
executionRunExportConfig = Channel.fromPath("${baseDir}/conf/Execution_Run_For_Output_Bag.json")
if (params.source == "dev") {
@@ -239,8 +240,9 @@ process getData {
tag "${repRID}"
input:
+ path bdbagConfig
path script_bdbagFetch
- path cookies from bdbag
+ path cookies, stageAs: "deriva-cookies.txt" from bdbag
path inputBag from inputBag_getData
output:
@@ -256,10 +258,10 @@ process getData {
ulimit -a >> ${repRID}.getData.log
# link deriva cookie for authentication
- echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log
- mkdir -p ~/.bdbag
- cp `readlink -e cookies.txt` ~/.bdbag/deriva-cookies.txt
- echo -e "LOG: linked" >> ${repRID}.getData.log
+ #echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log
+ #mkdir -p ~/.bdbag
+ #cp `readlink -e cookies.txt` ~/.bdbag/deriva-cookies.txt
+ #echo -e "LOG: linked" >> ${repRID}.getData.log
# get bag basename
replicate=\$(basename "${inputBag}")
diff --git a/workflow/scripts/bdbag_fetch.sh b/workflow/scripts/bdbag_fetch.sh
index 45ee14a..59e1136 100644
--- a/workflow/scripts/bdbag_fetch.sh
+++ b/workflow/scripts/bdbag_fetch.sh
@@ -9,7 +9,7 @@ then
n=0
until [ "${n}" -ge "3" ]
do
- bdbag --resolve-fetch missing --validate full ${1} --debug && validate=$(tail -n validate.txt | grep -o 'is valid') && break
+ bdbag --resolve-fetch missing --validate full ${1} --debug --config-file bdbag.json && validate=$(tail -n validate.txt | grep -o 'is valid') && break
n=$((n+1))
sleep 15
done
@@ -22,4 +22,4 @@ for i in $(find */ -name "*[_.]R[1-2].fastq.gz")
do
path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
cp ${i} ./${path}
-done
\ No newline at end of file
+done
--
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