Mercurial > repos > bebatut > data_manager_metaphlan2_database_downloader
changeset 6:27d7d61ca8df draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_metaphlan2_database_downloader commit bad4bb2f4bae0689a583c96d54193b937a340bb8-dirty
| author | bebatut |
|---|---|
| date | Tue, 21 Feb 2017 06:25:56 -0500 |
| parents | 6ef96ebbea92 |
| children | c2480b29f64e |
| files | data_manager/data_manager_metaphlan2_download.py data_manager_conf.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/data_manager_metaphlan2_download.py Tue Feb 21 05:40:07 2017 -0500 +++ b/data_manager/data_manager_metaphlan2_download.py Tue Feb 21 06:25:56 2017 -0500 @@ -105,7 +105,8 @@ dict( dbkey=build, value=today.isoformat(), - name="MetaPhlAn2 clade-specific marker genes")) + name="MetaPhlAn2 clade-specific marker genes"), + path=db_target_dir) if __name__ == "__main__": @@ -147,5 +148,6 @@ # Write output JSON print("Outputting JSON") print(str(json.dumps(data_tables))) - open(jsonfile, 'wb').write(json.dumps(data_tables)) + with open(jsonfile, 'wb') as out: + out.write(json.dumps(data_tables)) print("Done.")
--- a/data_manager_conf.xml Tue Feb 21 05:40:07 2017 -0500 +++ b/data_manager_conf.xml Tue Feb 21 06:25:56 2017 -0500 @@ -10,7 +10,7 @@ <move type="directory" relativize_symlinks="True"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">metaphlan2/data/${dbkey}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/metaphlan2/data/${dbkey}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/metaphlan2/data/${dbkey}/metaphlan2/data/</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>