Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/launch_instance @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
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2 # Copyright (c) 2009 Chris Moyer http://coredumped.org/
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3 #
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4 # Permission is hereby granted, free of charge, to any person obtaining a
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5 # copy of this software and associated documentation files (the
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6 # "Software"), to deal in the Software without restriction, including
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7 # without limitation the rights to use, copy, modify, merge, publish, dis-
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8 # tribute, sublicense, and/or sell copies of the Software, and to permit
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9 # persons to whom the Software is furnished to do so, subject to the fol-
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10 # lowing conditions:
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11 #
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12 # The above copyright notice and this permission notice shall be included
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13 # in all copies or substantial portions of the Software.
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14 #
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15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
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17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
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18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
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21
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22 #
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23 # Utility to launch an EC2 Instance
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24 #
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25 VERSION="0.2"
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26
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27
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28 CLOUD_INIT_SCRIPT = """#!/usr/bin/env python
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29 f = open("/etc/boto.cfg", "w")
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30 f.write(\"\"\"%s\"\"\")
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31 f.close()
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32 """
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33 import boto.pyami.config
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34 import boto.utils
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35 import re, os
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36 from boto.compat import ConfigParser
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37
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38 class Config(boto.pyami.config.Config):
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39 """A special config class that also adds import abilities
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40 Directly in the config file. To have a config file import
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41 another config file, simply use "#import <path>" where <path>
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42 is either a relative path or a full URL to another config
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43 """
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44
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45 def __init__(self):
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46 ConfigParser.__init__(self, {'working_dir' : '/mnt/pyami', 'debug' : '0'})
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47
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48 def add_config(self, file_url):
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49 """Add a config file to this configuration
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50 :param file_url: URL for the file to add, or a local path
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51 :type file_url: str
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52 """
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53 if not re.match("^([a-zA-Z0-9]*:\/\/)(.*)", file_url):
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54 if not file_url.startswith("/"):
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55 file_url = os.path.join(os.getcwd(), file_url)
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56 file_url = "file://%s" % file_url
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57 (base_url, file_name) = file_url.rsplit("/", 1)
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58 base_config = boto.utils.fetch_file(file_url)
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59 base_config.seek(0)
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60 for line in base_config.readlines():
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61 match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
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62 if match:
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63 self.add_config("%s/%s" % (base_url, match.group(1)))
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64 base_config.seek(0)
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65 self.readfp(base_config)
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66
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67 def add_creds(self, ec2):
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68 """Add the credentials to this config if they don't already exist"""
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69 if not self.has_section('Credentials'):
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70 self.add_section('Credentials')
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71 self.set('Credentials', 'aws_access_key_id', ec2.aws_access_key_id)
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72 self.set('Credentials', 'aws_secret_access_key', ec2.aws_secret_access_key)
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73
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74
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75 def __str__(self):
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76 """Get config as string"""
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77 from StringIO import StringIO
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78 s = StringIO()
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79 self.write(s)
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80 return s.getvalue()
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81
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82 SCRIPTS = []
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83
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84 def scripts_callback(option, opt, value, parser):
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85 arg = value.split(',')
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86 if len(arg) == 1:
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87 SCRIPTS.append(arg[0])
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88 else:
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89 SCRIPTS.extend(arg)
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90 setattr(parser.values, option.dest, SCRIPTS)
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91
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92 def add_script(scr_url):
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93 """Read a script and any scripts that are added using #import"""
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94 base_url = '/'.join(scr_url.split('/')[:-1]) + '/'
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95 script_raw = boto.utils.fetch_file(scr_url)
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96 script_content = ''
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97 for line in script_raw.readlines():
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98 match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
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99 #if there is an import
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100 if match:
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101 #Read the other script and put it in that spot
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102 script_content += add_script("%s/%s" % (base_url, match.group(1)))
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103 else:
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104 #Otherwise, add the line and move on
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105 script_content += line
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106 return script_content
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107
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108 if __name__ == "__main__":
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109 try:
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110 import readline
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111 except ImportError:
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112 pass
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113 import sys
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114 import time
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115 import boto
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116 from boto.ec2 import regions
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117 from optparse import OptionParser
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118 from boto.mashups.iobject import IObject
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119 parser = OptionParser(version=VERSION, usage="%prog [options] config_url")
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120 parser.add_option("-c", "--max-count", help="Maximum number of this type of instance to launch", dest="max_count", default="1")
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121 parser.add_option("--min-count", help="Minimum number of this type of instance to launch", dest="min_count", default="1")
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122 parser.add_option("--cloud-init", help="Indicates that this is an instance that uses 'CloudInit', Ubuntu's cloud bootstrap process. This wraps the config in a shell script command instead of just passing it in directly", dest="cloud_init", default=False, action="store_true")
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diff changeset
123 parser.add_option("-g", "--groups", help="Security Groups to add this instance to", action="append", dest="groups")
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124 parser.add_option("-a", "--ami", help="AMI to launch", dest="ami_id")
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parents:
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125 parser.add_option("-t", "--type", help="Type of Instance (default m1.small)", dest="type", default="m1.small")
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126 parser.add_option("-k", "--key", help="Keypair", dest="key_name")
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127 parser.add_option("-z", "--zone", help="Zone (default us-east-1a)", dest="zone", default="us-east-1a")
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diff changeset
128 parser.add_option("-r", "--region", help="Region (default us-east-1)", dest="region", default="us-east-1")
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129 parser.add_option("-i", "--ip", help="Elastic IP", dest="elastic_ip")
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130 parser.add_option("-n", "--no-add-cred", help="Don't add a credentials section", default=False, action="store_true", dest="nocred")
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diff changeset
131 parser.add_option("--save-ebs", help="Save the EBS volume on shutdown, instead of deleting it", default=False, action="store_true", dest="save_ebs")
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diff changeset
132 parser.add_option("-w", "--wait", help="Wait until instance is running", default=False, action="store_true", dest="wait")
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diff changeset
133 parser.add_option("-d", "--dns", help="Returns public and private DNS (implicates --wait)", default=False, action="store_true", dest="dns")
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parents:
diff changeset
134 parser.add_option("-T", "--tag", help="Set tag", default=None, action="append", dest="tags", metavar="key:value")
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diff changeset
135 parser.add_option("-s", "--scripts", help="Pass in a script or a folder containing scripts to be run when the instance starts up, assumes cloud-init. Specify scripts in a list specified by commas. If multiple scripts are specified, they are run lexically (A good way to ensure they run in the order is to prefix filenames with numbers)", type='string', action="callback", callback=scripts_callback)
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diff changeset
136 parser.add_option("--role", help="IAM Role to use, this implies --no-add-cred", dest="role")
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137
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138 (options, args) = parser.parse_args()
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139
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140 if len(args) < 1:
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141 parser.print_help()
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142 sys.exit(1)
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143 file_url = os.path.expanduser(args[0])
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144
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145 cfg = Config()
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146 cfg.add_config(file_url)
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147
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148 for r in regions():
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diff changeset
149 if r.name == options.region:
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parents:
diff changeset
150 region = r
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diff changeset
151 break
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152 else:
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153 print("Region %s not found." % options.region)
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diff changeset
154 sys.exit(1)
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parents:
diff changeset
155 ec2 = boto.connect_ec2(region=region)
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parents:
diff changeset
156 if not options.nocred and not options.role:
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diff changeset
157 cfg.add_creds(ec2)
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parents:
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158
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diff changeset
159 iobj = IObject()
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diff changeset
160 if options.ami_id:
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parents:
diff changeset
161 ami = ec2.get_image(options.ami_id)
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parents:
diff changeset
162 else:
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parents:
diff changeset
163 ami_id = options.ami_id
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parents:
diff changeset
164 l = [(a, a.id, a.location) for a in ec2.get_all_images()]
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diff changeset
165 ami = iobj.choose_from_list(l, prompt='Choose AMI')
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166
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parents:
diff changeset
167 if options.key_name:
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diff changeset
168 key_name = options.key_name
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diff changeset
169 else:
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diff changeset
170 l = [(k, k.name, '') for k in ec2.get_all_key_pairs()]
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parents:
diff changeset
171 key_name = iobj.choose_from_list(l, prompt='Choose Keypair').name
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diff changeset
172
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parents:
diff changeset
173 if options.groups:
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diff changeset
174 groups = options.groups
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diff changeset
175 else:
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diff changeset
176 groups = []
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diff changeset
177 l = [(g, g.name, g.description) for g in ec2.get_all_security_groups()]
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parents:
diff changeset
178 g = iobj.choose_from_list(l, prompt='Choose Primary Security Group')
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parents:
diff changeset
179 while g != None:
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diff changeset
180 groups.append(g)
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diff changeset
181 l.remove((g, g.name, g.description))
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parents:
diff changeset
182 g = iobj.choose_from_list(l, prompt='Choose Additional Security Group (0 to quit)')
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parents:
diff changeset
183
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diff changeset
184 user_data = str(cfg)
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diff changeset
185 # If it's a cloud init AMI,
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diff changeset
186 # then we need to wrap the config in our
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parents:
diff changeset
187 # little wrapper shell script
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188
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diff changeset
189 if options.cloud_init:
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diff changeset
190 user_data = CLOUD_INIT_SCRIPT % user_data
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parents:
diff changeset
191 scriptuples = []
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parents:
diff changeset
192 if options.scripts:
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parents:
diff changeset
193 scripts = options.scripts
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diff changeset
194 scriptuples.append(('user_data', user_data))
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parents:
diff changeset
195 for scr in scripts:
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parents:
diff changeset
196 scr_url = scr
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diff changeset
197 if not re.match("^([a-zA-Z0-9]*:\/\/)(.*)", scr_url):
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parents:
diff changeset
198 if not scr_url.startswith("/"):
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parents:
diff changeset
199 scr_url = os.path.join(os.getcwd(), scr_url)
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parents:
diff changeset
200 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
201 newfiles = os.listdir(scr_url)
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parents:
diff changeset
202 for f in newfiles:
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parents:
diff changeset
203 #put the scripts in the folder in the array such that they run in the correct order
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parents:
diff changeset
204 scripts.insert(scripts.index(scr) + 1, scr.split("/")[-1] + "/" + f)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
205 except OSError:
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parents:
diff changeset
206 scr_url = "file://%s" % scr_url
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parents:
diff changeset
207 try:
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parents:
diff changeset
208 scriptuples.append((scr, add_script(scr_url)))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
209 except Exception as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
210 pass
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parents:
diff changeset
211
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parents:
diff changeset
212 user_data = boto.utils.write_mime_multipart(scriptuples, compress=True)
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parents:
diff changeset
213
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parents:
diff changeset
214 shutdown_proc = "terminate"
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parents:
diff changeset
215 if options.save_ebs:
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parents:
diff changeset
216 shutdown_proc = "save"
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parents:
diff changeset
217
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parents:
diff changeset
218 instance_profile_name = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
219 if options.role:
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shellac
parents:
diff changeset
220 instance_profile_name = options.role
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shellac
parents:
diff changeset
221
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
222 r = ami.run(min_count=int(options.min_count), max_count=int(options.max_count),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
223 key_name=key_name, user_data=user_data,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
224 security_groups=groups, instance_type=options.type,
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parents:
diff changeset
225 placement=options.zone, instance_initiated_shutdown_behavior=shutdown_proc,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
226 instance_profile_name=instance_profile_name)
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shellac
parents:
diff changeset
227
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parents:
diff changeset
228 instance = r.instances[0]
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parents:
diff changeset
229
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parents:
diff changeset
230 if options.tags:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
231 for tag_pair in options.tags:
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shellac
parents:
diff changeset
232 name = tag_pair
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shellac
parents:
diff changeset
233 value = ''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
234 if ':' in tag_pair:
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shellac
parents:
diff changeset
235 name, value = tag_pair.split(':', 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
236 instance.add_tag(name, value)
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shellac
parents:
diff changeset
237
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
238 if options.dns:
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shellac
parents:
diff changeset
239 options.wait = True
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shellac
parents:
diff changeset
240
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
241 if not options.wait:
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shellac
parents:
diff changeset
242 sys.exit(0)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
243
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244 while True:
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245 instance.update()
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246 if instance.state == 'running':
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247 break
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248 time.sleep(3)
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249
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250 if options.dns:
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251 print("Public DNS name: %s" % instance.public_dns_name)
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252 print("Private DNS name: %s" % instance.private_dns_name)