diff --git a/charcoal/genbank_genomes.py b/charcoal/genbank_genomes.py index 00eef4d..663e923 100755 --- a/charcoal/genbank_genomes.py +++ b/charcoal/genbank_genomes.py @@ -20,6 +20,8 @@ def url_for_accession(accession): number = "/".join([number[p : p + 3] for p in range(0, len(number), 3)]) url = f"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/{db}/{number}" + print(f'downloading genome from: {url}') + with urllib.request.urlopen(url) as response: all_names = response.read() diff --git a/environment.yml b/environment.yml index 0b464b1..65ccf79 100644 --- a/environment.yml +++ b/environment.yml @@ -4,8 +4,8 @@ channels: - bioconda - defaults dependencies: - - python>=3.7 - - snakemake-minimal=6.4.1 + - python>=3.7,<3.10 + - snakemake-minimal==6.10.0 - screed - click>=7,<8 - pip diff --git a/setup.py b/setup.py index 1f7a25f..722036d 100644 --- a/setup.py +++ b/setup.py @@ -33,5 +33,5 @@ setup_requires = [ "setuptools>=38.6.0", 'setuptools_scm', 'setuptools_scm_git_archive' ], use_scm_version = {"write_to": "charcoal/version.py"}, - install_requires = ['snakemake==6.4.1', 'click>=7,<8'] + install_requires = ['snakemake==6.10.0', 'click>=7,<8'] )