python package

PRIDE-Archive · Jan 26, 2024 · ee1e664 · ee1e664
1 parent e37d786
commit ee1e664
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/parser/process_dataset.py b/parser/process_dataset.py
@@ -246,6 +246,7 @@ def convert_dir(local_dir, project_identifier,writer_method, nopeaklist=False):
     parser.add_argument('-w', '--writer', help='Save data to database or API')
     try:
         logger.info("process_dataset.py is running!")
+        print("process_dataset.py is running!")
         main(parser.parse_args())
         sys.exit(0)
     except Exception as ex:

diff --git a/scripts/runDataset.sh b/scripts/runDataset.sh
@@ -48,6 +48,7 @@ fi
 
 DATE=$(date +"%Y%m%d%H%M")
 LOG_FILE_NAME="${JOB_NAME}/${PROJECT_ACCESSION}-${DATE}.log"
+LOG_FILE_ERROR_NAME="${JOB_NAME}/${PROJECT_ACCESSION}-${DATE}-error.log"
 JOB_NAME="${JOB_NAME}-${PROJECT_ACCESSION}"
 
 
@@ -65,6 +66,6 @@ sbatch -t 7-0 \
      --mail-type=ALL \
      --mail-user=${JOB_EMAIL} \
      --job-name=${JOB_NAME} \
-     -o /dev/null \
-     -e /dev/null \
-     --wrap="python3 process_dataset -p ${PROJECT_ACCESSION} --dontdelete -w api"
+     -o ${LOG_FILE_NAME} \
+     -e ${LOG_FILE_ERROR_NAME} \
+     --wrap="process_dataset -p ${PROJECT_ACCESSION} --dontdelete -w api"