From b6175498daa9ec5d6dc66b3438c5b7657455a958 Mon Sep 17 00:00:00 2001 From: jfsanchezherrero Date: Fri, 4 Mar 2022 15:49:28 +0100 Subject: [PATCH] updates --- BacterialTyper/config/install_dependencies.py | 4 ++-- BacterialTyper/scripts/species_identification_KMA.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/BacterialTyper/config/install_dependencies.py b/BacterialTyper/config/install_dependencies.py index 3892cc0..72f3b60 100644 --- a/BacterialTyper/config/install_dependencies.py +++ b/BacterialTyper/config/install_dependencies.py @@ -158,7 +158,7 @@ def install(software, min_version, install_path, Debug): print() ## create symbolic link in bin directory in environment - HCGB_main.get_symbolic_link(file_list, env_bin_directory) + HCGB_files.get_symbolic_link(file_list, env_bin_directory) print(colored("**Software (%s - Version: %s) installed in the system and add it to $PATH environment variable." %(software, versionInstalled),'green')) return (versionInstalled) @@ -380,7 +380,7 @@ def install_binary(folder_software, site, install_path, Debug): ## check if file already available compress_file_name = os.path.join(install_path, site.rsplit('/', 1)[-1]) - if not HCGB_main.is_non_zero_file(compress_file_name): + if not HCGB_files.is_non_zero_file(compress_file_name): ## download HCGB_sys.wget_download(site, install_path) diff --git a/BacterialTyper/scripts/species_identification_KMA.py b/BacterialTyper/scripts/species_identification_KMA.py index 22f6076..0a5f073 100644 --- a/BacterialTyper/scripts/species_identification_KMA.py +++ b/BacterialTyper/scripts/species_identification_KMA.py @@ -258,8 +258,8 @@ def check_db_indexed(index_name, folder): print ("\t\t** %s days ago" %days_passed) ## download again if (days_passed > 60): - print ("\t\t** Downloading information again just to be sure...") - return(False) + print ("\t\t** Downloading information again is recommended just to be sure...") + #return(False) ## dump in screen names = index_name + '.name'