Mercurial > repos > shellac > guppy_basecaller
comparison env/bin/asadmin @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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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 | |
2 # Copyright (c) 2011 Joel Barciauskas http://joel.barciausk.as/ | |
3 # | |
4 # Permission is hereby granted, free of charge, to any person obtaining a | |
5 # copy of this software and associated documentation files (the | |
6 # "Software"), to deal in the Software without restriction, including | |
7 # without limitation the rights to use, copy, modify, merge, publish, dis- | |
8 # tribute, sublicense, and/or sell copies of the Software, and to permit | |
9 # persons to whom the Software is furnished to do so, subject to the fol- | |
10 # lowing conditions: | |
11 # | |
12 # The above copyright notice and this permission notice shall be included | |
13 # in all copies or substantial portions of the Software. | |
14 # | |
15 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS | |
16 # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL- | |
17 # ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT | |
18 # SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, | |
19 # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
20 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS | |
21 | |
22 # | |
23 # Auto Scaling Groups Tool | |
24 # | |
25 VERSION="0.1" | |
26 usage = """%prog [options] [command] | |
27 Commands: | |
28 list|ls List all Auto Scaling Groups | |
29 list-lc|ls-lc List all Launch Configurations | |
30 delete <name> Delete ASG <name> | |
31 delete-lc <name> Delete Launch Configuration <name> | |
32 get <name> Get details of ASG <name> | |
33 create <name> Create an ASG | |
34 create-lc <name> Create a Launch Configuration | |
35 update <name> <prop> <value> Update a property of an ASG | |
36 update-image <asg-name> <lc-name> Update image ID for ASG by creating a new LC | |
37 migrate-instances <name> Shut down current instances one by one and wait for ASG to start up a new instance with the current AMI (useful in conjunction with update-image) | |
38 | |
39 Examples: | |
40 | |
41 1) Create launch configuration | |
42 bin/asadmin create-lc my-lc-1 -i ami-1234abcd -t c1.xlarge -k my-key -s web-group -m | |
43 | |
44 2) Create auto scaling group in us-east-1a and us-east-1c with a load balancer and min size of 2 and max size of 6 | |
45 bin/asadmin create my-asg -z us-east-1a -z us-east-1c -l my-lc-1 -b my-lb -H ELB -p 180 -x 2 -X 6 | |
46 """ | |
47 | |
48 def get_group(autoscale, name): | |
49 g = autoscale.get_all_groups(names=[name]) | |
50 if len(g) < 1: | |
51 print "No auto scaling groups by the name of %s found" % name | |
52 return sys.exit(1) | |
53 return g[0] | |
54 | |
55 def get_lc(autoscale, name): | |
56 l = autoscale.get_all_launch_configurations(names=[name]) | |
57 if len(l) < 1: | |
58 print "No launch configurations by the name of %s found" % name | |
59 sys.exit(1) | |
60 return l[0] | |
61 | |
62 def list(autoscale): | |
63 """List all ASGs""" | |
64 print "%-20s %s" % ("Name", "LC Name") | |
65 print "-"*80 | |
66 groups = autoscale.get_all_groups() | |
67 for g in groups: | |
68 print "%-20s %s" % (g.name, g.launch_config_name) | |
69 | |
70 def list_lc(autoscale): | |
71 """List all LCs""" | |
72 print "%-30s %-20s %s" % ("Name", "Image ID", "Instance Type") | |
73 print "-"*80 | |
74 for l in autoscale.get_all_launch_configurations(): | |
75 print "%-30s %-20s %s" % (l.name, l.image_id, l.instance_type) | |
76 | |
77 def get(autoscale, name): | |
78 """Get details about ASG <name>""" | |
79 g = get_group(autoscale, name) | |
80 print "="*80 | |
81 print "%-30s %s" % ('Name:', g.name) | |
82 print "%-30s %s" % ('Launch configuration:', g.launch_config_name) | |
83 print "%-30s %s" % ('Minimum size:', g.min_size) | |
84 print "%-30s %s" % ('Maximum size:', g.max_size) | |
85 print "%-30s %s" % ('Desired capacity:', g.desired_capacity) | |
86 print "%-30s %s" % ('Load balancers:', ','.join(g.load_balancers)) | |
87 | |
88 print | |
89 | |
90 print "Instances" | |
91 print "---------" | |
92 print "%-20s %-20s %-20s %s" % ("ID", "Status", "Health", "AZ") | |
93 for i in g.instances: | |
94 print "%-20s %-20s %-20s %s" % \ | |
95 (i.instance_id, i.lifecycle_state, i.health_status, i.availability_zone) | |
96 | |
97 print | |
98 | |
99 def create(autoscale, name, zones, lc_name, load_balancers, hc_type, hc_period, | |
100 min_size, max_size, cooldown, capacity): | |
101 """Create an ASG named <name>""" | |
102 g = AutoScalingGroup(name=name, launch_config=lc_name, | |
103 availability_zones=zones, load_balancers=load_balancers, | |
104 default_cooldown=cooldown, health_check_type=hc_type, | |
105 health_check_period=hc_period, desired_capacity=capacity, | |
106 min_size=min_size, max_size=max_size) | |
107 g = autoscale.create_auto_scaling_group(g) | |
108 return list(autoscale) | |
109 | |
110 def create_lc(autoscale, name, image_id, instance_type, key_name, | |
111 security_groups, instance_monitoring): | |
112 l = LaunchConfiguration(name=name, image_id=image_id, | |
113 instance_type=instance_type,key_name=key_name, | |
114 security_groups=security_groups, | |
115 instance_monitoring=instance_monitoring) | |
116 l = autoscale.create_launch_configuration(l) | |
117 return list_lc(autoscale) | |
118 | |
119 def update(autoscale, name, prop, value): | |
120 g = get_group(autoscale, name) | |
121 setattr(g, prop, value) | |
122 g.update() | |
123 return get(autoscale, name) | |
124 | |
125 def delete(autoscale, name, force_delete=False): | |
126 """Delete this ASG""" | |
127 g = get_group(autoscale, name) | |
128 autoscale.delete_auto_scaling_group(g.name, force_delete) | |
129 print "Auto scaling group %s deleted" % name | |
130 return list(autoscale) | |
131 | |
132 def delete_lc(autoscale, name): | |
133 """Delete this LC""" | |
134 l = get_lc(autoscale, name) | |
135 autoscale.delete_launch_configuration(name) | |
136 print "Launch configuration %s deleted" % name | |
137 return list_lc(autoscale) | |
138 | |
139 def update_image(autoscale, name, lc_name, image_id, is_migrate_instances=False): | |
140 """ Get the current launch config, | |
141 Update its name and image id | |
142 Re-create it as a new launch config | |
143 Update the ASG with the new LC | |
144 Delete the old LC """ | |
145 | |
146 g = get_group(autoscale, name) | |
147 l = get_lc(autoscale, g.launch_config_name) | |
148 | |
149 old_lc_name = l.name | |
150 l.name = lc_name | |
151 l.image_id = image_id | |
152 autoscale.create_launch_configuration(l) | |
153 g.launch_config_name = l.name | |
154 g.update() | |
155 | |
156 if(is_migrate_instances): | |
157 migrate_instances(autoscale, name) | |
158 else: | |
159 return get(autoscale, name) | |
160 | |
161 def migrate_instances(autoscale, name): | |
162 """ Shut down instances of the old image type one by one | |
163 and let the ASG start up instances with the new image """ | |
164 g = get_group(autoscale, name) | |
165 | |
166 old_instances = g.instances | |
167 ec2 = boto.connect_ec2() | |
168 for old_instance in old_instances: | |
169 print "Terminating instance " + old_instance.instance_id | |
170 ec2.terminate_instances([old_instance.instance_id]) | |
171 while True: | |
172 g = get_group(autoscale, name) | |
173 new_instances = g.instances | |
174 for new_instance in new_instances: | |
175 hasOldInstance = False | |
176 instancesReady = True | |
177 if(old_instance.instance_id == new_instance.instance_id): | |
178 hasOldInstance = True | |
179 print "Waiting for old instance to shut down..." | |
180 break | |
181 elif(new_instance.lifecycle_state != 'InService'): | |
182 instancesReady = False | |
183 print "Waiting for instances to be ready...." | |
184 break | |
185 if(not hasOldInstance and instancesReady): | |
186 break | |
187 else: | |
188 time.sleep(20) | |
189 return get(autoscale, name) | |
190 | |
191 if __name__ == "__main__": | |
192 try: | |
193 import readline | |
194 except ImportError: | |
195 pass | |
196 import boto | |
197 import sys | |
198 import time | |
199 from optparse import OptionParser | |
200 from boto.mashups.iobject import IObject | |
201 from boto.ec2.autoscale import AutoScalingGroup | |
202 from boto.ec2.autoscale import LaunchConfiguration | |
203 parser = OptionParser(version=VERSION, usage=usage) | |
204 """ Create launch config options """ | |
205 parser.add_option("-i", "--image-id", | |
206 help="Image (AMI) ID", action="store", | |
207 type="string", default=None, dest="image_id") | |
208 parser.add_option("-t", "--instance-type", | |
209 help="EC2 Instance Type (e.g., m1.large, c1.xlarge), default is m1.large", | |
210 action="store", type="string", default="m1.large", dest="instance_type") | |
211 parser.add_option("-k", "--key-name", | |
212 help="EC2 Key Name", | |
213 action="store", type="string", dest="key_name") | |
214 parser.add_option("-s", "--security-group", | |
215 help="EC2 Security Group", | |
216 action="append", default=[], dest="security_groups") | |
217 parser.add_option("-m", "--monitoring", | |
218 help="Enable instance monitoring", | |
219 action="store_true", default=False, dest="instance_monitoring") | |
220 | |
221 """ Create auto scaling group options """ | |
222 parser.add_option("-z", "--zone", help="Add availability zone", action="append", default=[], dest="zones") | |
223 parser.add_option("-l", "--lc-name", | |
224 help="Launch configuration name", | |
225 action="store", default=None, type="string", dest="lc_name") | |
226 parser.add_option("-b", "--load-balancer", | |
227 help="Load balancer name", | |
228 action="append", default=[], dest="load_balancers") | |
229 parser.add_option("-H", "--health-check-type", | |
230 help="Health check type (EC2 or ELB)", | |
231 action="store", default="EC2", type="string", dest="hc_type") | |
232 parser.add_option("-p", "--health-check-period", | |
233 help="Health check period in seconds (default 300s)", | |
234 action="store", default=300, type="int", dest="hc_period") | |
235 parser.add_option("-X", "--max-size", | |
236 help="Max size of ASG (default 10)", | |
237 action="store", default=10, type="int", dest="max_size") | |
238 parser.add_option("-x", "--min-size", | |
239 help="Min size of ASG (default 2)", | |
240 action="store", default=2, type="int", dest="min_size") | |
241 parser.add_option("-c", "--cooldown", | |
242 help="Cooldown time after a scaling activity in seconds (default 300s)", | |
243 action="store", default=300, type="int", dest="cooldown") | |
244 parser.add_option("-C", "--desired-capacity", | |
245 help="Desired capacity of the ASG", | |
246 action="store", default=None, type="int", dest="capacity") | |
247 parser.add_option("-f", "--force", | |
248 help="Force delete ASG", | |
249 action="store_true", default=False, dest="force") | |
250 parser.add_option("-y", "--migrate-instances", | |
251 help="Automatically migrate instances to new image when running update-image", | |
252 action="store_true", default=False, dest="migrate_instances") | |
253 | |
254 (options, args) = parser.parse_args() | |
255 | |
256 if len(args) < 1: | |
257 parser.print_help() | |
258 sys.exit(1) | |
259 | |
260 autoscale = boto.connect_autoscale() | |
261 | |
262 print "%s" % (autoscale.region.endpoint) | |
263 | |
264 command = args[0].lower() | |
265 if command in ("ls", "list"): | |
266 list(autoscale) | |
267 elif command in ("ls-lc", "list-lc"): | |
268 list_lc(autoscale) | |
269 elif command == "get": | |
270 get(autoscale, args[1]) | |
271 elif command == "create": | |
272 create(autoscale, args[1], options.zones, options.lc_name, | |
273 options.load_balancers, options.hc_type, | |
274 options.hc_period, options.min_size, options.max_size, | |
275 options.cooldown, options.capacity) | |
276 elif command == "create-lc": | |
277 create_lc(autoscale, args[1], options.image_id, options.instance_type, | |
278 options.key_name, options.security_groups, | |
279 options.instance_monitoring) | |
280 elif command == "update": | |
281 update(autoscale, args[1], args[2], args[3]) | |
282 elif command == "delete": | |
283 delete(autoscale, args[1], options.force) | |
284 elif command == "delete-lc": | |
285 delete_lc(autoscale, args[1]) | |
286 elif command == "update-image": | |
287 update_image(autoscale, args[1], args[2], | |
288 options.image_id, options.migrate_instances) | |
289 elif command == "migrate-instances": | |
290 migrate_instances(autoscale, args[1]) |