--- a/env/bin/launch_instance	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,252 +0,0 @@
-#!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
-# Copyright (c) 2009 Chris Moyer http://coredumped.org/
-#
-# Permission is hereby granted, free of charge, to any person obtaining a
-# copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish, dis-
-# tribute, sublicense, and/or sell copies of the Software, and to permit
-# persons to whom the Software is furnished to do so, subject to the fol-
-# lowing conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABIL-
-# ITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
-# SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 
-# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-
-#
-# Utility to launch an EC2 Instance
-#
-VERSION="0.2"
-
-
-CLOUD_INIT_SCRIPT = """#!/usr/bin/env python
-f = open("/etc/boto.cfg", "w")
-f.write(\"\"\"%s\"\"\")
-f.close()
-"""
-import boto.pyami.config
-import boto.utils
-import re, os
-from boto.compat import ConfigParser
-
-class Config(boto.pyami.config.Config):
-    """A special config class that also adds import abilities
-    Directly in the config file. To have a config file import
-    another config file, simply use "#import <path>" where <path>
-    is either a relative path or a full URL to another config
-    """
-
-    def __init__(self):
-        ConfigParser.__init__(self, {'working_dir' : '/mnt/pyami', 'debug' : '0'})
-
-    def add_config(self, file_url):
-        """Add a config file to this configuration
-        :param file_url: URL for the file to add, or a local path
-        :type file_url: str
-        """
-        if not re.match("^([a-zA-Z0-9]*:\/\/)(.*)", file_url):
-            if not file_url.startswith("/"):
-                file_url = os.path.join(os.getcwd(), file_url)
-            file_url = "file://%s" % file_url
-        (base_url, file_name) = file_url.rsplit("/", 1)
-        base_config = boto.utils.fetch_file(file_url)
-        base_config.seek(0)
-        for line in base_config.readlines():
-            match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
-            if match:
-                self.add_config("%s/%s" % (base_url, match.group(1)))
-        base_config.seek(0)
-        self.readfp(base_config)
-
-    def add_creds(self, ec2):
-        """Add the credentials to this config if they don't already exist"""
-        if not self.has_section('Credentials'):
-            self.add_section('Credentials')
-            self.set('Credentials', 'aws_access_key_id', ec2.aws_access_key_id)
-            self.set('Credentials', 'aws_secret_access_key', ec2.aws_secret_access_key)
-
-
-    def __str__(self):
-        """Get config as string"""
-        from StringIO import StringIO
-        s = StringIO()
-        self.write(s)
-        return s.getvalue()
-
-SCRIPTS = []
-
-def scripts_callback(option, opt, value, parser):
-    arg = value.split(',')
-    if len(arg) == 1:
-        SCRIPTS.append(arg[0])
-    else:
-        SCRIPTS.extend(arg)
-    setattr(parser.values, option.dest, SCRIPTS)
-
-def add_script(scr_url):
-    """Read a script and any scripts that are added using #import"""
-    base_url = '/'.join(scr_url.split('/')[:-1]) + '/'
-    script_raw = boto.utils.fetch_file(scr_url)
-    script_content = ''
-    for line in script_raw.readlines():
-        match = re.match("^#import[\s\t]*([^\s^\t]*)[\s\t]*$", line)
-        #if there is an import
-        if match:
-            #Read the other script and put it in that spot
-            script_content += add_script("%s/%s" % (base_url, match.group(1)))
-        else:
-            #Otherwise, add the line and move on
-            script_content += line
-    return script_content
-
-if __name__ == "__main__":
-    try:
-        import readline
-    except ImportError:
-        pass
-    import sys
-    import time
-    import boto
-    from boto.ec2 import regions
-    from optparse import OptionParser
-    from boto.mashups.iobject import IObject
-    parser = OptionParser(version=VERSION, usage="%prog [options] config_url")
-    parser.add_option("-c", "--max-count", help="Maximum number of this type of instance to launch", dest="max_count", default="1")
-    parser.add_option("--min-count", help="Minimum number of this type of instance to launch", dest="min_count", default="1")
-    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")
-    parser.add_option("-g", "--groups", help="Security Groups to add this instance to",  action="append", dest="groups")
-    parser.add_option("-a", "--ami", help="AMI to launch", dest="ami_id")
-    parser.add_option("-t", "--type", help="Type of Instance (default m1.small)", dest="type", default="m1.small")
-    parser.add_option("-k", "--key", help="Keypair", dest="key_name")
-    parser.add_option("-z", "--zone", help="Zone (default us-east-1a)", dest="zone", default="us-east-1a")
-    parser.add_option("-r", "--region", help="Region (default us-east-1)", dest="region", default="us-east-1")
-    parser.add_option("-i", "--ip", help="Elastic IP", dest="elastic_ip")
-    parser.add_option("-n", "--no-add-cred", help="Don't add a credentials section", default=False, action="store_true", dest="nocred")
-    parser.add_option("--save-ebs", help="Save the EBS volume on shutdown, instead of deleting it", default=False, action="store_true", dest="save_ebs")
-    parser.add_option("-w", "--wait", help="Wait until instance is running", default=False, action="store_true", dest="wait")
-    parser.add_option("-d", "--dns", help="Returns public and private DNS (implicates --wait)", default=False, action="store_true", dest="dns")
-    parser.add_option("-T", "--tag", help="Set tag", default=None, action="append", dest="tags", metavar="key:value")
-    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)
-    parser.add_option("--role", help="IAM Role to use, this implies --no-add-cred", dest="role")
-
-    (options, args) = parser.parse_args()
-
-    if len(args) < 1:
-        parser.print_help()
-        sys.exit(1)
-    file_url = os.path.expanduser(args[0])
-
-    cfg = Config()
-    cfg.add_config(file_url)
-
-    for r in regions():
-        if r.name == options.region:
-            region = r
-            break
-    else:
-        print("Region %s not found." % options.region)
-        sys.exit(1)
-    ec2 = boto.connect_ec2(region=region)
-    if not options.nocred and not options.role:
-        cfg.add_creds(ec2)
-
-    iobj = IObject()
-    if options.ami_id:
-        ami = ec2.get_image(options.ami_id)
-    else:
-        ami_id = options.ami_id
-        l = [(a, a.id, a.location) for a in ec2.get_all_images()]
-        ami = iobj.choose_from_list(l, prompt='Choose AMI')
-
-    if options.key_name:
-        key_name = options.key_name
-    else:
-        l = [(k, k.name, '') for k in ec2.get_all_key_pairs()]
-        key_name = iobj.choose_from_list(l, prompt='Choose Keypair').name
-
-    if options.groups:
-        groups = options.groups
-    else:
-        groups = []
-        l = [(g, g.name, g.description) for g in ec2.get_all_security_groups()]
-        g = iobj.choose_from_list(l, prompt='Choose Primary Security Group')
-        while g != None:
-            groups.append(g)
-            l.remove((g, g.name, g.description))
-            g = iobj.choose_from_list(l, prompt='Choose Additional Security Group (0 to quit)')
-
-    user_data = str(cfg)
-    # If it's a cloud init AMI,
-    # then we need to wrap the config in our
-    # little wrapper shell script
-
-    if options.cloud_init:
-        user_data = CLOUD_INIT_SCRIPT % user_data
-        scriptuples = []
-        if options.scripts:
-            scripts = options.scripts
-            scriptuples.append(('user_data', user_data))
-            for scr in scripts:
-                scr_url = scr
-                if not re.match("^([a-zA-Z0-9]*:\/\/)(.*)", scr_url):
-                    if not scr_url.startswith("/"):
-                        scr_url = os.path.join(os.getcwd(), scr_url)
-                    try:
-                        newfiles = os.listdir(scr_url)
-                        for f in newfiles:
-                            #put the scripts in the folder in the array such that they run in the correct order
-                            scripts.insert(scripts.index(scr) + 1, scr.split("/")[-1] + "/" + f)
-                    except OSError:
-                        scr_url = "file://%s" % scr_url
-                try:
-                    scriptuples.append((scr, add_script(scr_url)))
-                except Exception as e:
-                    pass
-
-            user_data = boto.utils.write_mime_multipart(scriptuples, compress=True)
-
-    shutdown_proc = "terminate"
-    if options.save_ebs:
-        shutdown_proc = "save"
-
-    instance_profile_name = None
-    if options.role:
-        instance_profile_name = options.role
-
-    r = ami.run(min_count=int(options.min_count), max_count=int(options.max_count),
-            key_name=key_name, user_data=user_data,
-            security_groups=groups, instance_type=options.type,
-            placement=options.zone, instance_initiated_shutdown_behavior=shutdown_proc,
-            instance_profile_name=instance_profile_name)
-
-    instance = r.instances[0]
-
-    if options.tags:
-        for tag_pair in options.tags:
-            name = tag_pair
-            value = ''
-            if ':' in tag_pair:
-                name, value = tag_pair.split(':', 1)
-            instance.add_tag(name, value)
-
-    if options.dns:
-        options.wait = True
-
-    if not options.wait:
-        sys.exit(0)
-
-    while True:
-        instance.update()
-        if instance.state == 'running':
-            break
-        time.sleep(3)
-
-    if options.dns:
-        print("Public DNS name: %s" % instance.public_dns_name)
-        print("Private DNS name: %s" % instance.private_dns_name)