added credentials.

mahmudhera · Aug 31, 2022 · 384198d · 384198d
1 parent eda032d
commit 384198d
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diff --git a/experiments/test_experiment/workflow_test_expt.sh b/experiments/test_experiment/workflow_test_expt.sh
@@ -27,7 +27,7 @@ thresholdBP=50  # this has the largest impact on FNs and FPs: setting it higher
 
 # download genomes
 echo "$scriptDir/get_reference_genomes.py -n $numGenomes -s $dataDir  -u"
-$scriptDir/get_reference_genomes.py -n $numGenomes -s $dataDir  -u
+$scriptDir/get_reference_genomes.py -n $numGenomes -s $dataDir -u -c mahmudhera93@gmail.com
 
 # create the full genome reference database
 echo "$scriptDir/create_genome_ref_db.py $genomePath $genomeDatabaseFull $numGenomesFullDB"

diff --git a/scripts/get_reference_genomes.py b/scripts/get_reference_genomes.py
@@ -212,11 +212,15 @@ def main():
             cmd = 'rm -rf ' + path+'/'+current_directory_name
             subprocess.call(cmd.split(' '))
 
+            print('Trying to reconnect...')
             helper.is_connected = False
             while not helper.is_connected:
                 helper.connect()
+            print('Connection reestablished.')
+
             helper.return_to_original_direct()
             continue
+
         total_downloaded += 1
         helper.return_to_original_direct()