From da7d18895476d4140564af96b21fc982544728e6 Mon Sep 17 00:00:00 2001
From: Kirill Tsukanov <ktsukanov@ebi.ac.uk>
Date: Fri, 11 Oct 2019 12:25:53 +0100
Subject: [PATCH] Increase memory for trait mapping; remove --unattended flag

---
 bin/trait_mapping.py             | 5 +----
 docs/submit-opentargets-batch.md | 6 +++---
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/bin/trait_mapping.py b/bin/trait_mapping.py
index f17f9ca7..68cf0634 100644
--- a/bin/trait_mapping.py
+++ b/bin/trait_mapping.py
@@ -9,7 +9,7 @@ def launch():
 
     main.main(parser.input_filepath, parser.output_mappings_filepath,
               parser.output_curation_filepath, parser.filters, parser.zooma_host,
-              parser.oxo_target_list, parser.oxo_distance, parser.unattended)
+              parser.oxo_target_list, parser.oxo_distance)
 
 
 class ArgParser:
@@ -39,8 +39,6 @@ def __init__(self, argv):
                             help="target ontologies to use with OxO")
         parser.add_argument("-d", dest="oxo_distance", default=3,
                             help="distance to use to query OxO.")
-        parser.add_argument('-u', dest="unattended", action='store_true',
-                            help="unattended launch, hide ETA estimates")
 
         args = parser.parse_args(args=argv[1:])
 
@@ -55,7 +53,6 @@ def __init__(self, argv):
         self.zooma_host = args.zooma_host
         self.oxo_target_list = [target.strip() for target in args.oxo_target_list.split(",")]
         self.oxo_distance = args.oxo_distance
-        self.unattended = args.unattended
 
 
 if __name__ == '__main__':
diff --git a/docs/submit-opentargets-batch.md b/docs/submit-opentargets-batch.md
index bb98b06e..087cf0b0 100644
--- a/docs/submit-opentargets-batch.md
+++ b/docs/submit-opentargets-batch.md
@@ -87,7 +87,7 @@ A new Java package will be generated in the directory `clinvar-xml-parser/src/ma
 Here we transform ClinVar's XML file into a JSON file which can be parsed by the downstream tools, using an XML parser which we (if necessary) updated during the previous step.
 
 ```bash
-cd ${CODE_ROOT} && ${BSUB_CMDLINE} -M 4G \
+cd ${CODE_ROOT} && ${BSUB_CMDLINE} -n 8 -M 4G \
   -o ${BATCH_ROOT}/logs/convert_clinvar_files.out \
   -e ${BATCH_ROOT}/logs/convert_clinvar_files.err \
   java -jar ${CODE_ROOT}/clinvar-xml-parser/target/clinvar-parser-1.0-SNAPSHOT-jar-with-dependencies.jar \
@@ -168,10 +168,10 @@ The TSV file eventually returned by OpenTargets has these columns:
 See information about the trait mapping pipeline [here](trait-mapping-pipeline.md). It is run with the following command:
 
 ```bash
-cd ${CODE_ROOT} && ${BSUB_CMDLINE} \
+cd ${CODE_ROOT} && ${BSUB_CMDLINE} -M 4G \
   -o ${BATCH_ROOT}/logs/trait_mapping.out \
   -e ${BATCH_ROOT}/logs/trait_mapping.err \
-  python bin/trait_mapping.py -u \
+  python bin/trait_mapping.py \
   -i ${BATCH_ROOT}/clinvar/clinvar.filtered.json.gz \
   -o ${BATCH_ROOT}/trait_mapping/automated_trait_mappings.tsv \
   -c ${BATCH_ROOT}/trait_mapping/traits_requiring_curation.tsv