Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 86:07790b77b3c7 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bded7bac774cdcf890076c055f72a48710ce638b-dirty"
| author | dfornika |
|---|---|
| date | Fri, 05 Nov 2021 22:51:43 +0000 |
| parents | 7316cb684753 |
| children | |
| files | data_manager/kraken2_build_database.py |
| diffstat | 1 files changed, 8 insertions(+), 10 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.py Fri Nov 05 22:45:02 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 22:51:43 2021 +0000 @@ -151,12 +151,11 @@ standard_prebuilt_size_url = size_to_url_str[standard_prebuilt_size] # download the pre-built database try: - src = urlopen( - 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard%s_%s.tar.gz' - % (standard_prebuilt_size_url, date_url_str) - ) + download_url = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard%s_%s.tar.gz' % (standard_prebuilt_size_url, date_url_str) + src = urlopen(download_url) except URLError as e: - print(e, sys.stderr) + print('url: ' + download_url, file=sys.stderr) + print(e, file=sys.stderr) exit(1) with open('tmp_data.tar.gz', 'wb') as dst: @@ -205,12 +204,11 @@ # download the minikraken2 data try: - src = urlopen( - 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' - % minikraken2_version - ) + download_url = 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' % minikraken2_version + src = urlopen(download_url) except URLError as e: - print(e, sys.stderr) + print('url: ' + download_url, file=sys.stderr) + print(e, file=sys.stderr) exit(1) with open('tmp_data.tar.gz', 'wb') as dst: