Mercurial > repos > dfornika > data_manager_build_kraken2_database

changeset 5:2eb7850c7434 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty
author dfornika
date Wed, 27 Feb 2019 21:32:42 -0500
parents 9f918cce82b2
children 2ea60e272b90
files data_manager/kraken2_standard_database_builder.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/kraken2_standard_database_builder.xml	Wed Feb 27 21:21:30 2019 -0500
+++ b/data_manager/kraken2_standard_database_builder.xml	Wed Feb 27 21:32:42 2019 -0500
@@ -7,16 +7,16 @@
     <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
-	export KRAKEN2_DB_NAME="`date --iso-8601`_standard" &&
+	#set kraken2_db_name = datetime.datetime.today().strftime('%Y-%m-%d')
         mkdir kraken2_database && cd kraken2_database &&
         kraken2-build \
           --standard \
-          --db $KRAKEN2_DB_NAME \
+          --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>