Mercurial > repos > iuc > data_manager_interproscan

comparison data_manager/interproscan.py @ 3:0df47f8552f6 draft default tip

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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
comparison
equal deleted inserted replaced
2:7776cb18fdf8 3:0df47f8552f6
77 raise RuntimeError("Version '%s' is not valid" % args.version) 77 raise RuntimeError("Version '%s' is not valid" % args.version)
78 tag = args.version 78 tag = args.version
79 else: 79 else:
80 tag = all_tags[-1] 80 tag = all_tags[-1]
81 81
82 setup_script = 'initial_setup.py'
83 sub_version = re.match(r"^[0-9]\.([0-9]{2})-[0-9]{2}\.[0-9]$", tag)
84 if sub_version and len(sub_version.groups()) == 1 and int(sub_version.group(1)) >= 58:
85 # The setup script was renamed in 5.58
86 setup_script = 'setup.py'
87 else:
88 raise RuntimeError("Sorry, this data manager can only download data for InterProScan >= 5.58-91.0. Use the 0.0.2 version for older versions of InterProScan.")
89
82 print("Will download data for InterProScan version: %s" % tag) 90 print("Will download data for InterProScan version: %s" % tag)
83 91
84 print("Getting MD5 checksum:") 92 print("Getting MD5 checksum:")
85 md5 = requests.get(url=MD5_URL.format(version=tag)).text 93 md5 = requests.get(url=MD5_URL.format(version=tag)).text
86 if not re.match(r"^([a-fA-F\d]{32}) interproscan-[0-9]\.[0-9]{2}-[0-9]{2}\.[0-9]-64-bit.tar.gz$", md5): 94 if not re.match(r"^([a-fA-F\d]{32}) interproscan-[0-9]\.[0-9]{2}-[0-9]{2}\.[0-9]-64-bit.tar.gz$", md5):
123 131
124 print("Done, removing tarball and unneeded files...") 132 print("Done, removing tarball and unneeded files...")
125 os.remove(dest_tar) 133 os.remove(dest_tar)
126 shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag)) 134 shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag))
127 135
128 print("Running initial_setup.py (index hmm models)...") 136 print("Running {} (index hmm models)...".format(setup_script))
129 # Write a temp properties file in work dir 137 # Write a temp properties file in work dir
130 prop_file_src = os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'interproscan.properties') 138 prop_file_src = os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'interproscan.properties')
131 with open(prop_file_src, 'r') as prop: 139 with open(prop_file_src, 'r') as prop:
132 prop_content = prop.read() 140 prop_content = prop.read()
133 prop_content = re.sub(r'^data\.directory=.*$', 'data.directory=%s' % os.path.join(output_directory, 'data'), prop_content, flags=re.M) 141 prop_content = re.sub(r'^data\.directory=.*$', 'data.directory=%s' % os.path.join(output_directory, 'data'), prop_content, flags=re.M)
134 with open('interproscan.properties', 'w') as prop: 142 with open('interproscan.properties', 'w') as prop:
135 prop.write(prop_content) 143 prop.write(prop_content)
136 # Run the index command 144 # Run the index command
137 cmd_args = [os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'initial_setup.py')] 145 cmd_args = [os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), setup_script), 'interproscan.properties']
138 proc = subprocess.Popen(args=cmd_args, shell=False) 146 proc = subprocess.Popen(args=cmd_args, shell=False)
139 out, err = proc.communicate() 147 out, err = proc.communicate()
140 print(out) 148 print(out)
141 print(err, file=sys.stderr) 149 print(err, file=sys.stderr)
142 return_code = proc.wait() 150 return_code = proc.wait()
143 if return_code: 151 if return_code:
144 print("Error running initial_setup.py.", file=sys.stderr) 152 print("Error running {}.".format(setup_script), file=sys.stderr)
145 sys.exit(return_code) 153 sys.exit(return_code)
146 154
147 data_manager_dict["data_tables"][args.datatable_name].append( 155 data_manager_dict["data_tables"][args.datatable_name].append(
148 dict( 156 dict(
149 value=tag, 157 value=tag,