| Previous changeset 84:0132e84d8572 (2021-11-05) Next changeset 86:07790b77b3c7 (2021-11-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bded7bac774cdcf890076c055f72a48710ce638b-dirty" |
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modified:
data_manager/kraken2_build_database.py |
| b |
| diff -r 0132e84d8572 -r 7316cb684753 data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Fri Nov 05 22:37:45 2021 +0000 +++ b/data_manager/kraken2_build_database.py Fri Nov 05 22:45:02 2021 +0000 |
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| @@ -16,8 +16,10 @@ try: # Python3 from urllib.request import urlopen + from urllib.error import URLError except ImportError: from urllib2 import urlopen + from urllib2 import URLError DATA_TABLE_NAME = "kraken2_databases" @@ -148,10 +150,15 @@ date_url_str = prebuilt_date.replace('-', '') standard_prebuilt_size_url = size_to_url_str[standard_prebuilt_size] # download the pre-built database - src = urlopen( - 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard%s_%s.tar.gz' - % (standard_prebuilt_size_url, date_url_str) - ) + try: + src = urlopen( + 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard%s_%s.tar.gz' + % (standard_prebuilt_size_url, date_url_str) + ) + except URLError as e: + print(e, sys.stderr) + exit(1) + with open('tmp_data.tar.gz', 'wb') as dst: shutil.copyfileobj(src, dst) # unpack the downloaded archive to the target directory @@ -197,10 +204,15 @@ database_path = database_value # download the minikraken2 data - src = urlopen( - 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' - % minikraken2_version - ) + try: + src = urlopen( + 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' + % minikraken2_version + ) + except URLError as e: + print(e, sys.stderr) + exit(1) + with open('tmp_data.tar.gz', 'wb') as dst: shutil.copyfileobj(src, dst) # unpack the downloaded archive to the target directory |