Commit 77c0cffe authored by jcorvi's avatar jcorvi

Update run_gitlab-runner.sh

parent 3a1edcf2
Pipeline #12379 failed with stage
in 2 seconds
......@@ -9,8 +9,6 @@ pipeline_path="/home/jcorvi/projects/etransafe/etransafe-text-mining-pipeline/pi
input_dir="/home/jcorvi/eTRANSAFE_DATA/workshop_data/gitlab-ci/input/"
#set the home/work dir of the pipeline
base_dir="/home/jcorvi/eTRANSAFE_DATA/workshop_data/gitlab-ci/"`date '+%d-%m-%Y'`
echo "prueba de echo y variable de entorno"
echo $DB_SERVER
#Database connection details
#set server and port
db_server=$DB_SERVER
......@@ -25,6 +23,6 @@ db_collection_prefix="dev"`date '+%d-%m-%Y'`
#The complete mongo uri
db_uri="mongodb://"$db_user":"$db_password"@"$db_server":"$db_port"/?authSource="$db_name"&authMechanism=SCRAM-SHA-1"
echo $db_uri
#command
$nextflow_path run $pipeline_path --inputDir $input_dir --baseDir $base_dir --db_uri $db_uri --db_name $db_name --db_collection_prefix $db_collection_prefix -with-report $base_dir/report.html -with-trace -with-timeline $base_dir/timeline.html -name $pipeline_name
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