# HG changeset patch
# User dfornika
# Date 1551322203 18000
# Node ID 2ea60e272b907e0bfa24810287d4a25d7f75dcb7
# Parent  2eb7850c74346079c359f34d77714b8416c9c339
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty

diff -r 2eb7850c7434 -r 2ea60e272b90 data_manager/kraken2_standard_database_builder.xml
--- a/data_manager/kraken2_standard_database_builder.xml	Wed Feb 27 21:32:42 2019 -0500
+++ b/data_manager/kraken2_standard_database_builder.xml	Wed Feb 27 21:50:03 2019 -0500
@@ -7,16 +7,18 @@
     <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-	#set kraken2_db_name = datetime.datetime.today().strftime('%Y-%m-%d')
+        #import datetime
+	#set kraken2_db_name = datetime.date.today().strftime('%Y-%m-%d')
         mkdir kraken2_database && cd kraken2_database &&
         kraken2-build \
           --standard \
-          --db ${kraken2_db_name} \
-          --kmer-len ${kmer_len} \
-          --minimizer-len ${minimizer_len} \
-          --minimizer-spaces ${minimizer_spaces} &&
+	  --threads \${GALAXY_SLOTS:-1} \
+          --db '${kraken2_db_name}' \
+          --kmer-len '${kmer_len}' \
+          --minimizer-len '${minimizer_len}' \
+          --minimizer-spaces '${minimizer_spaces}' &&
         cd .. &&
-        python '$__tool_directory__/make_json.py' --db ${kraken2_db_name} --out '${out_file}'
+        python '$__tool_directory__/make_json.py' --db '${kraken2_db_name}' --out '${out_file}'
     ]]>
     </command>
     <inputs>