Mercurial > repos > bebatut > data_manager_sortmerna_database_downloader
changeset 14:b39e50b428cb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit b4a2d79d49c731753ff38ce6f27a2a97f5af28b9-dirty
author | bebatut |
---|---|
date | Tue, 13 Jun 2017 02:26:20 -0400 |
parents | b93a11966024 |
children | |
files | data_manager/data_manager_sortmerna_download.py data_manager/data_manager_sortmerna_download.xml |
diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/data_manager_sortmerna_download.py Mon Jun 12 11:36:09 2017 -0400 +++ b/data_manager/data_manager_sortmerna_download.py Tue Jun 13 02:26:20 2017 -0400 @@ -4,6 +4,7 @@ import argparse import json import os +import shutil import tarfile import requests import subprocess @@ -134,7 +135,7 @@ fasta_filepath = os.path.join(filedir, "%s.fasta" % db_name) indexed_filepath = os.path.join(filedir, db_name) # Move the fasta file - os.rename(input_filepath, fasta_filepath) + shutil.move(input_filepath, fasta_filepath) # Index the file with indexdb_rna command = "indexdb_rna --ref %s,%s" % ( fasta_filepath, @@ -210,7 +211,6 @@ data_tables, args.version, target_dir) - print(os.listdir(target_dir)) # Write output JSON print("Outputting JSON")
--- a/data_manager/data_manager_sortmerna_download.xml Mon Jun 12 11:36:09 2017 -0400 +++ b/data_manager/data_manager_sortmerna_download.xml Tue Jun 13 02:26:20 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.2" tool_type="manage_data"> +<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.1" tool_type="manage_data"> <description>reference databases</description> <macros> <import>macros.xml</import>