Mercurial > repos > iuc > data_manager_interproscan
diff data_manager/interproscan.py @ 3:0df47f8552f6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036
author | iuc |
---|---|
date | Wed, 07 Dec 2022 13:41:38 +0000 |
parents | 0db4f153d86d |
children |
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--- a/data_manager/interproscan.py Tue Feb 01 17:56:03 2022 +0000 +++ b/data_manager/interproscan.py Wed Dec 07 13:41:38 2022 +0000 @@ -79,6 +79,14 @@ else: tag = all_tags[-1] + setup_script = 'initial_setup.py' + sub_version = re.match(r"^[0-9]\.([0-9]{2})-[0-9]{2}\.[0-9]$", tag) + if sub_version and len(sub_version.groups()) == 1 and int(sub_version.group(1)) >= 58: + # The setup script was renamed in 5.58 + setup_script = 'setup.py' + else: + raise RuntimeError("Sorry, this data manager can only download data for InterProScan >= 5.58-91.0. Use the 0.0.2 version for older versions of InterProScan.") + print("Will download data for InterProScan version: %s" % tag) print("Getting MD5 checksum:") @@ -125,7 +133,7 @@ os.remove(dest_tar) shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag)) - print("Running initial_setup.py (index hmm models)...") + print("Running {} (index hmm models)...".format(setup_script)) # Write a temp properties file in work dir prop_file_src = os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'interproscan.properties') with open(prop_file_src, 'r') as prop: @@ -134,14 +142,14 @@ with open('interproscan.properties', 'w') as prop: prop.write(prop_content) # Run the index command - cmd_args = [os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'initial_setup.py')] + cmd_args = [os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), setup_script), 'interproscan.properties'] proc = subprocess.Popen(args=cmd_args, shell=False) out, err = proc.communicate() print(out) print(err, file=sys.stderr) return_code = proc.wait() if return_code: - print("Error running initial_setup.py.", file=sys.stderr) + print("Error running {}.".format(setup_script), file=sys.stderr) sys.exit(return_code) data_manager_dict["data_tables"][args.datatable_name].append(