| Previous changeset 1:1316375a8cbb (2017-03-13) Next changeset 3:854d9862a9f1 (2017-08-01) |
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Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit f474a24a52dcda7fb6681869e24f566d28f1e457 |
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modified:
data_manager/data_manager_humann2_download.py data_manager/data_manager_humann2_download.xml |
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| diff -r 1316375a8cbb -r 6112a571f012 data_manager/data_manager_humann2_download.py --- a/data_manager/data_manager_humann2_download.py Mon Mar 13 12:34:20 2017 -0400 +++ b/data_manager/data_manager_humann2_download.py Fri Jun 23 06:00:47 2017 -0400 |
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| @@ -5,6 +5,7 @@ import json import optparse import os +import shutil import subprocess import sys @@ -15,7 +16,7 @@ "uniref50_diamond": "Full UniRef50", "uniref50_ec_filtered_diamond": "EC-filtered UniRef50", "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2", - "uniref90_diamond": "Full UniRef50", + "uniref90_diamond": "Full UniRef90", "uniref90_ec_filtered_diamond": "EC-filtered UniRef90", "DEMO_diamond": "Demo" } @@ -112,13 +113,12 @@ db_target_dir = os.path.join(target_dir, database) build_target_dir = os.path.join(db_target_dir, build) os.makedirs(build_target_dir) - cmd = "humann2_databases --download %s %s %s" % (database, - build, - db_target_dir) + cmd = "humann2_databases --download %s %s %s --update-config no" % ( + database, + build, + db_target_dir) subprocess.check_call(cmd, shell=True) - print(os.listdir(db_target_dir)) - os.rename(os.path.join(db_target_dir, database), build_target_dir) - print(os.listdir(db_target_dir)) + shutil.move(os.path.join(db_target_dir, database), build_target_dir) add_data_table_entry( data_tables, table_name, |
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| diff -r 1316375a8cbb -r 6112a571f012 data_manager/data_manager_humann2_download.xml --- a/data_manager/data_manager_humann2_download.xml Mon Mar 13 12:34:20 2017 -0400 +++ b/data_manager/data_manager_humann2_download.xml Fri Jun 23 06:00:47 2017 -0400 |
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| @@ -1,7 +1,10 @@ -<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data"> +<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="@VERSION@.0" tool_type="manage_data"> <description>Download HUMAnN2 database</description> + <macros> + <token name="@VERSION@">0.9.9</token> + </macros> <requirements> - <requirement type="package" version="0.9.9">humann2</requirement> + <requirement type="package" version="@VERSION@">humann2</requirement> </requirements> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> @@ -30,7 +33,7 @@ <option value="uniref50_diamond">Full UniRef50</option> <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option> <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option> - <option value="uniref90_diamond" selected="true">Full UniRef50</option> + <option value="uniref90_diamond" selected="true">Full UniRef90</option> <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option> <option value="DEMO_diamond">Demo</option> </param> |