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bcs-3rd-generation-gene-sequence-data-assembly.yml
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bcs-3rd-generation-gene-sequence-data-assembly.yml
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ROSTemplateFormatVersion: '2015-09-01'
Description:
zh-cn: 此模板部署了WDL-Canu三代基因组组装方案，通过创建VPC、安全组、ECS实例、NAS文件系统、OSS存储桶及RAM用户等资源，实现了基于批量计算服务的基因数据自动处理环境，支持高效基因组序列组装。
en: This template deploys the WDL-Canu third-generation genome assembly pipeline,
establishing an automated genomic data processing environment based on Batch Compute
services by provisioning resources such as a Virtual Private Cloud (VPC), Security
Groups, Elastic Compute Service (ECS) instances, Network Attached Storage (NAS)
file systems, Object Storage Service (OSS) buckets, and Resource Access Management
(RAM) users, thereby facilitating efficient genomic sequence assembly.
Parameters:
VpcCidrBlock:
Type: String
Label:
en: VPC CIDR Block
zh-cn: 专有网络网段
Description:
en: 'The IP address range of the VPC in the CIDR Block form; <br>you can use
the following IP address ranges: <br><font color=''green''>[10.0.0.0/8]</font><br><font
color=''green''>[172.16.0.0/12]</font><br><font color=''green''>[192.168.0.0/16]</font>'
zh-cn: 专有网络IP地址段范围，<br>您可以使用以下的IP地址段:<br><font color='green'>[10.0.0.0/8]</font><br><font
color='green'>[172.16.0.0/12]</font><br><font color='green'>[192.168.0.0/16]</font>
Default: 192.168.0.0/16
AllowedValues:
- 192.168.0.0/16
- 172.16.0.0/12
- 10.0.0.0/8
VSwitchZoneId:
Type: String
Label:
en: VSwitch Availability Zone
zh-cn: 交换机可用区
Description:
en: Availability Zone ID,<br><b>note： <font color='blue'>Before selecting, please
confirm that the Availability Zone supports the specification of creating
ECS resources</font></b>
zh-cn: 可用区ID，<br><b>注： <font color='blue'>选择可用区前请确认该可用区是否支持创建ECS资源的规格</font></b>
AssociationProperty: ALIYUN::ECS::Instance:ZoneId
VSwitchCidrBlock:
Type: String
Label:
en: VSwitch CIDR Block
zh-cn: 交换机网段
Description:
en: Must be a sub-network segment of the proprietary network and is not occupied
by other VSwitches.
zh-cn: 必须是所属专有网络的子网段，并且没有被其他交换机占用。
Default: 192.168.0.0/24
EipBandwidth:
Type: Number
Label:
en: EIP Bandwidth
zh-cn: 弹性IP带宽峰值
Description:
en: 'Value range: [0, 1000], Unit: Mbps.'
zh-cn: 取值范围：[0, 1000]，单位：Mbps。
Default: 5
MinValue: 1
MaxValue: 1000
EcsImageId:
Type: String
Label:
en: Image
zh-cn: 镜像
Description:
en: 'Server instance Image ID. <br>Cloud Market Image Name: BatchCompute Cromwell
server<br>Version：v1.3<br>[Beijing: <font color=''green''>m-2zedp42auazn4ywxalq8</font>]<br>[Shenzhen:
<font color=''green''>m-wz9cvcpip06f5urnyeeh</font>]<br>[Zhangjiakou: <font
color=''green''>m-8vb4j0sovjhf46zmcd4f</font>]<br>[Hohhot: <font color=''green''>m-hp31anaw1u4emcyialqq</font>]<br>[Hangzhou:
<font color=''green''>m-bp10s23s69igzv4zbx1e</font>]<br>[Shanghai: <font color=''green''>m-uf6ey0i1b0ctp427qu1x</font>]<br>[Hong
Kong: <font color=''green''>m-j6c4qiobdapkh606g3y4</font>]<br>[Qingdao: <font
color=''green''>m-m5eegtbul3dj94q9fv01</font>]<br>note: The above image is
for the reference of users of China stations only, such as international stations
or other geographical users needs, Please mention the repair order; <br>see
detail: <b><a href=''https://marketplace.alibabacloud.com/products/'' target=''_blank''><font
color=''blue''>Cloud Market Image</font></a></b>'
zh-cn: '服务器镜像<br>云市场镜像名称： BatchCompute Cromwell server<br>版本：v1.3<br>[北京: <font
color=''green''>m-2zedp42auazn4ywxalq8</font>]<br>[深圳: <font color=''green''>m-wz9cvcpip06f5urnyeeh</font>]<br>[张家口:
<font color=''green''>m-8vb4j0sovjhf46zmcd4f</font>]<br>[呼和浩特: <font color=''green''>m-hp31anaw1u4emcyialqq</font>]<br>[杭州:
<font color=''green''>m-bp10s23s69igzv4zbx1e</font>]<br>[上海: <font color=''green''>m-uf6ey0i1b0ctp427qu1x</font>]<br>[香港:
<font color=''green''>m-j6c4qiobdapkh606g3y4</font>]<br>[青岛: <font color=''green''>m-m5eegtbul3dj94q9fv01</font>]<br>注：以上镜像仅供中国站用户参考，如国际站或其他地域用户需求时，请提供工单；<br>详见：<b><a
href=''https://market.aliyun.com/products/?keywords=BatchCompute Cromwell
server'' target=''_blank''><font color=''blue''>BatchCompute Cromwell server镜像</font></a></b>'
EcsInstanceType:
Type: String
Label:
en: Instance Type
zh-cn: 实例规格
Description:
en: 'Fill in the specifications that can be used under the VSwitch availability
zone, and it is recommended that memory ECS is greater than 4CPUs16GiB specifications;</b></font><br>recommended
specifications：<font color=''red''><b>ecs.r5.xlarge</b></font><br>note: a
few zones do not support recommended specifications<br>see detail: <a href=''https://www.alibabacloud.com/help/en/doc-detail/25378.html''
target=''_blank''><b><font color=''blue''>Instance Specification Family</font></a></b>'
zh-cn: 填写VSwitch可用区下可使用的规格；建议使用内存型ECS大于4CPUs16GiB的规格；<br>推荐规格：<font color='red'><b>ecs.r5.xlarge</b></font><br>注：可用区可能不支持推荐规格<br>规格详见：<a
href='https://help.aliyun.com/document_detail/25378.html' target='_blank'><b><font
color='blue'>实例规格族</font></a></b>
AssociationProperty: ALIYUN::ECS::Instance::InstanceType
AssociationPropertyMetadata:
ZoneId: VSwitchZoneId
EcsSystemDiskCategory:
Type: String
Label:
en: System Disk Type
zh-cn: 系统盘类型
Description:
en: '<font color=''blue''><b>Optional values:</b></font><br>[cloud_efficiency:
<font color=''green''>Efficient Cloud Disk</font>]<br>[cloud_ssd: <font color=''green''>SSD
Cloud Disk</font>]<br>[cloud_essd: <font color=''green''>ESSD Cloud Disk</font>]<br>[cloud:
<font color=''green''>Cloud Disk</font>]<br>[ephemeral_ssd: <font color=''green''>Local
SSD Cloud Disk</font>]'
zh-cn: '<font color=''blue''><b>可选值：</b></font><br>[cloud_efficiency: <font
color=''green''>高效云盘</font>]<br>[cloud_ssd: <font color=''green''>SSD云盘</font>]<br>[cloud_essd:
<font color=''green''>ESSD云盘</font>]<br>[cloud: <font color=''green''>普通云盘</font>]<br>[ephemeral_ssd:
<font color=''green''>本地SSD盘</font>]'
Default: cloud_ssd
AllowedValues:
- cloud_efficiency
- cloud_ssd
- cloud
- cloud_essd
- ephemeral_ssd
EcsSystemDiskSize:
Type: Number
Label:
en: System Disk Space
zh-cn: 系统盘空间
Description:
en: 'System disk size, range of values: 40-500, units: GB.'
zh-cn: 系统盘大小, 取值范围：[40, 500], 单位：GB。
Default: 40
EcsPassword:
Type: String
Label:
en: Instance Password
zh-cn: 实例密码
Description:
en: Server login password, Length 8-30, must contain three(Capital letters,
lowercase letters, numbers, ()`~!@#$%^&*_-+=|{}[]:;'<>,.?/ Special symbol
in).
zh-cn: 服务器登录密码,长度8-30，必须包含三项（大写字母、小写字母、数字、 ()`~!@#$%^&*_-+=|{}[]:;'<>,.?/ 中的特殊符号）。
ConstraintDescription:
en: Length 8-30, must contain three(Capital letters, lowercase letters, numbers,
()`~!@#$%^&*_-+=|{}[]:;'<>,.?/ Special symbol in).
zh-cn: 长度8-30，必须包含三项（大写字母、小写字母、数字、 ()`~!@#$%^&*_-+=|{}[]:;'<>,.?/ 中的特殊符号）。
AllowedPattern: '[0-9A-Za-z\_\-\&:;''<>,=%`~!@#\(\)\$\^\*\+\|\{\}\[\]\.\?\/]+$'
MinLength: 8
MaxLength: 30
NoEcho: true
BucketName:
Type: String
Label:
en: Bucket Name
zh-cn: 存储空间名称
Description:
en: The name must be 3 to 63 bytes in length, The name must start and end with
a lowercase letter or digit.The name can contain only lowercase letters, digits,
and hyphens (-).;<br><b>note：<font color='blue'>A bucket name must be globally
unique within OSS. Bucket names cannot be changed after the bucket is created.</b></font>
zh-cn: 长度为3~63个字符，必须以小写字母或数字开头和结尾，可以包含小写字母、数字和连字符(-);<br><b>注：<font color='blue'>需要全网唯一性，已经存在的不能在创建</b></font>
Default: my-test-canu-oss
BucketDeletionForce:
Type: Boolean
Label:
en: Support for Force Deletion
zh-cn: 支持强制删除
Description:
en: Do you want to force the deletion of files in OSS?
zh-cn: 是否强制删除OSS中的文件
Default: false
UserName:
Type: String
Label:
en: Username
zh-cn: 用户名
Description:
en: Cannot be a user name that already exists, specify a user name, which can
contain up to 64 characters. Format:^[a-zA-Z0-9\.@\-_]+$ .
zh-cn: 不能是已经存在的用户名，最多包含64个字符。格式：^[a-zA-Z0-9\.@\-_]+$ 。
Default: gen_test
UserPassword:
Type: String
Label:
en: User Password
zh-cn: 用户密码
Description:
en: Specify password, 8-30 digits, password must meet password strength requirements,
composed of upper and lower case letters and Numbers.
zh-cn: 指定密码，8-30位，密码必须符合密码强度要求，由大小写字母和数字组成。
NoEcho: true
Resources:
EcsVpc:
Type: ALIYUN::ECS::VPC
Properties:
CidrBlock:
Ref: VpcCidrBlock
VpcName:
Fn::Join:
- '-'
- - StackId
- Ref: ALIYUN::StackId
Metadata:
ALIYUN::ROS::Designer:
id: 7ad2a34d-0519-4de2-a841-b0574f6f6f24
EcsSecurityGroup:
Type: ALIYUN::ECS::SecurityGroup
Properties:
VpcId:
Ref: EcsVpc
SecurityGroupIngress:
- IpProtocol: icmp
NicType: internet
PortRange: -1/-1
Priority: 1
SourceCidrIp: 0.0.0.0/0
- IpProtocol: tcp
NicType: intranet
PortRange: 3389/3389
Priority: 1
SourceCidrIp: 0.0.0.0/0
- IpProtocol: tcp
NicType: internet
PortRange: 22/22
Priority: 1
SourceCidrIp: 0.0.0.0/0
- IpProtocol: tcp
NicType: internet
PortRange: 8000/8000
Priority: 1
SourceCidrIp: 0.0.0.0/0
SecurityGroupName:
Fn::Join:
- _
- - StackId
- Ref: ALIYUN::StackId
Metadata:
ALIYUN::ROS::Designer:
id: 78b06052-62de-404c-9616-7696a3d31210
EcsVSwitch:
Type: ALIYUN::ECS::VSwitch
Properties:
ZoneId:
Ref: VSwitchZoneId
VpcId:
Ref: EcsVpc
CidrBlock:
Ref: VSwitchCidrBlock
VSwitchName:
Fn::Join:
- _
- - StackId
- Ref: ALIYUN::StackId
Metadata:
ALIYUN::ROS::Designer:
id: d7fe3883-f6fd-430d-965c-80ac0b8e6488
NasAccessGroup:
Type: ALIYUN::NAS::AccessGroup
Properties:
AccessGroupName:
Fn::Join:
- '-'
- - StackId
- Ref: ALIYUN::StackId
AccessGroupType: Vpc
Metadata:
ALIYUN::ROS::Designer:
id: 45bed963-d61e-44e4-ab2a-2e39a766c75c
NasFileSystem:
Type: ALIYUN::NAS::FileSystem
Properties:
ProtocolType: NFS
StorageType: Performance
Metadata:
ALIYUN::ROS::Designer:
id: 9500ceee-ea85-476e-9b4a-28f2c286aae7
NasMountTarget:
Type: ALIYUN::NAS::MountTarget
Properties:
VpcId:
Ref: EcsVpc
VSwitchId:
Ref: EcsVSwitch
AccessGroupName:
Ref: NasAccessGroup
FileSystemId:
Ref: NasFileSystem
NetworkType: Vpc
Metadata:
ALIYUN::ROS::Designer:
id: 9878d9af-497c-4bea-8981-6865fc52ea31
DepensOn:
- NasFileSystem
- NasAccessRule
OssBucket:
Type: ALIYUN::OSS::Bucket
Properties:
BucketName:
Ref: BucketName
DeletionForce:
Ref: BucketDeletionForce
Tags:
Key: best_practice
Value: '109'
Metadata:
ALIYUN::ROS::Designer:
id: 24c8f702-ddaa-4134-a6ea-4c6501fd4070
RamUser:
Type: ALIYUN::RAM::User
Properties:
LoginProfile:
Password:
Ref: UserPassword
PasswordResetRequired: false
Policies:
- PolicyDocument:
Statement:
- Action:
- ecs:*
- vpc:*HaVip*
- vpc:*RouteTable*
- vpc:*VRouter*
- vpc:*RouteEntry*
- vpc:*VSwitch*
- vpc:*Vpc*
- vpc:*Cen*
- vpc:*Tag*
- vpc:*NetworkAcl*
- vpc:*Eip*
- vpc:*HighDefinitionMonitor*
- rds:*
- nas:*
- oss:*
- batchcompute:*
- cr:Get*
- cr:List*
- cr:PullRepository
Effect: Allow
Resource:
- '*'
- Fn::Join:
- ''
- - 'acs:oss:*:*:'
- Ref: BucketName
- /genomics/*
- Action:
- dms:LoginDatabase
Effect: Allow
Resource:
- acs:rds:*:*:*
Version: '1'
PolicyName:
Fn::Join:
- '-'
- - StackId
- Ref: ALIYUN::StackId
UserName:
Ref: UserName
Metadata:
ALIYUN::ROS::Designer:
id: 63ca0ca8-d37f-4397-b554-cdf64ae522c7
RamAccessKey:
Type: ALIYUN::RAM::AccessKey
Properties:
UserName:
Ref: RamUser
DependsOn:
- RamUser
Metadata:
ALIYUN::ROS::Designer:
id: 471af498-a56a-495f-966a-c7c64d1726a3
EcsInstance:
Type: ALIYUN::ECS::InstanceGroup
Properties:
VpcId:
Ref: EcsVpc
VSwitchId:
Ref: EcsVSwitch
SecurityGroupId:
Ref: EcsSecurityGroup
ImageId:
Ref: EcsImageId
AllocatePublicIP: false
InstanceChargeType: PostPaid
InstanceName:
Fn::Join:
- ''
- - Canu-Cromwell
- -[1,3]
InstanceType:
Ref: EcsInstanceType
IoOptimized: optimized
MaxAmount: 1
Password:
Ref: EcsPassword
SystemDiskCategory:
Ref: EcsSystemDiskCategory
SystemDiskSize:
Ref: EcsSystemDiskSize
Tags:
- Key: best_practice
Value: '109'
UserData:
Fn::Replace:
- ros-notify:
Fn::GetAtt:
- RosWaitConditionHandle
- CurlCli
- Fn::Join:
- ''
- - "#!/bin/sh \n"
- "# set -e \n"
- "mkdir /root/tmp && cd /root/tmp && touch mount.sh && chmod +x mount.sh\
\ \n"
- "echo '#!/bin/bash'>> /root/tmp/mount.sh \n"
- echo '
- Fn::Join:
- ''
- - 'sudo mount -t nfs -o vers=4,minorversion=0,rsize=1048576,wsize=1048576,hard,timeo=600,retrans=2,noresvport '
- Fn::GetAtt:
- NasMountTarget
- MountTargetDomain
- ":/ /mnt \n"
- "'>> /root/tmp/mount.sh \n"
- "bash mount.sh \n"
- "export hostname=`hostname` \n"
- "sed -i '/127.0.0.1/d' /etc/hosts \n"
- "echo \"127.0.0.1 $hostname\" >> /etc/hosts \n"
- "echo '127.0.0.1 localhost' >> /etc/hosts \n"
- "cd /home/cromwell \n"
- export access_key_id=
- Fn::GetAtt:
- RamAccessKey
- AccessKeyId
- " \n"
- export access_key_secret=
- Fn::GetAtt:
- RamAccessKey
- AccessKeySecret
- " \n"
- export bucket_name=
- Fn::GetAtt:
- OssBucket
- Name
- " \n"
- export endpoint=
- Fn::Join:
- ''
- - http://oss-
- Ref: ALIYUN::Region
- -internal.aliyuncs.com
- " \n"
- "export bucket_dir='genomics/wdl' \n"
- "wget http://gosspublic.alicdn.com/ossutil/1.6.10/ossutil64 \n"
- "chmod 755 ossutil64 \n"
- "./ossutil64 config -k $access_key_secret -i $access_key_id -e $endpoint\
\ \n"
- ./ossutil64 mkdir oss://
- Ref: BucketName
- "/$bucket_dir/ \n"
- "cd /home/cromwell/docker-compose-mysql \n"
- "./server.sh init --id=$access_key_id --key=$access_key_secret --root=oss://$bucket_name/$bucket_dir\
\ --instance=ecs.sn1.medium --image=img-ubuntu-vpc & \n"
- "##cd /home/cromwell/docker-compose-mysql && ./server.sh stop & \n"
- "##cd /home/cromwell/docker-compose-mysql && ./server.sh start & \n"
- "cd /root/tmp && bash mount.sh \n"
- "cd /home/canu-1.8 \n"
- "sed -i '/\"vpc\"/d' canu_options.json \n"
- 'sed -i ''/"systemDisk"/a\ '
- Fn::Join:
- ''
- - '"vpc": "'
- Ref: VpcCidrBlock
- ' '
- Fn::GetAtt:
- EcsVpc
- VpcId
- '",'
- "' canu_options.json \n"
- "sed -i '/\"docker\"/d' canu_options.json \n"
- 'sed -i ''/"vpc"/a\ '
- Fn::Join:
- ''
- - '"docker": "'
- registry.
- Ref: ALIYUN::Region
- .aliyuncs.com/poc_test/canu:ovlv1.0",
- "' canu_options.json \n"
- "sed -i '/\"mounts\"/d' canu_options.json \n"
- 'sed -i ''/"docker"/a\ '
- Fn::Join:
- ''
- - '"mounts": "'
- nas://
- Fn::GetAtt:
- NasMountTarget
- MountTargetDomain
- :/ /mnt/ true",
- "' canu_options.json \n"
- "mkdir -p /mnt/canu \n"
- "wget https://ros-template-resources.oss-cn-beijing.aliyuncs.com/BCS/ecoli_p6_25x.filtered.fastq\
\ -O /mnt/canu/ecoli_p6_25x.filtered.fastq \n"
- "mkdir /root/tmp && cd /root/tmp && touch start_canu_task.sh && chmod\
\ +x start_canu_task.sh \n"
- "echo '#!/bin/bash' >> start_canu_task.sh \n"
- "echo 'cd /mnt/canu/' >> start_canu_task.sh \n"
- "echo '/home/canu-1.8/Linux-amd64/bin/canu -p ecoli -d ecoli-pacbio$RANDOM\
\ genomeSize=4.8m -pacbio-raw ecoli_p6_25x.filtered.fastq &' >> start_canu_task.sh\
\ \n"
- "#cd /root/tmp && ./start_canu_task.sh \n"
- "cd /mnt/canu/ \n"
- "/home/canu-1.8/Linux-amd64/bin/canu -p ecoli -d ecoli-pacbio$RANDOM\
\ genomeSize=4.8m -pacbio-raw ecoli_p6_25x.filtered.fastq & \n"
- "ros-notify -d \"{\\\"Data\\\" : \\\"Success\\\", \\\"Status\\\" : \\\
\"Success\\\"}\" \n"
DependsOn:
- NasMountTarget
- OssBucket
- RamAccessKey
Metadata:
ALIYUN::ROS::Designer:
id: 94b59b37-907d-4f92-875b-efc831a26625
NasAccessRule:
Type: ALIYUN::NAS::AccessRule
Properties:
AccessGroupName:
Ref: NasAccessGroup
SourceCidrIp: 0.0.0.0/0
Metadata:
ALIYUN::ROS::Designer:
id: 7ffe4548-b0e1-43f3-b50d-8977f514a017
DepensOn:
- NasAccessGroup
RosWaitConditionHandle:
Type: ALIYUN::ROS::WaitConditionHandle
Properties: {}
Metadata:
ALIYUN::ROS::Designer:
id: bb4463e0-3213-432a-9cc2-3e9cb1efdf12
RosWaitCondition:
Type: ALIYUN::ROS::WaitCondition
Properties:
Count: 1
Handle:
Ref: RosWaitConditionHandle
Timeout: 600
Metadata:
ALIYUN::ROS::Designer:
id: 04894ebe-ad5d-4338-a2d4-5577cdfdbe20
VpcEip:
Type: ALIYUN::VPC::EIP
Properties:
Bandwidth:
Ref: EipBandwidth
InternetChargeType: PayByTraffic
Metadata:
ALIYUN::ROS::Designer:
id: e03025bb-40a2-47de-8387-3fa9a5374eee
VpcEipAssociation:
Type: ALIYUN::VPC::EIPAssociation
Properties:
InstanceId:
Fn::Select:
- 0
- Fn::GetAtt:
- EcsInstance
- InstanceIds
AllocationId:
Ref: VpcEip
DependsOn: EcsInstance
Metadata:
ALIYUN::ROS::Designer:
id: 630cc4f3-0749-4f83-a87c-915267e22aa8
DependOn:
- EcsInstanceGroup
- VpcEip
Outputs:
CromwellServerUrl:
Value:
Fn::Join:
- ''
- - Fn::GetAtt:
- VpcEip
- EipAddress
- :8000
Eip:
Value:
Fn::GetAtt:
- VpcEip
- EipAddress
Metadata:
ALIYUN::ROS::Interface:
ParameterGroups:
- Parameters:
- VpcCidrBlock
- VSwitchZoneId
- VSwitchCidrBlock
- EipBandwidth
Label:
default: VPC
- Parameters:
- EcsImageId
- EcsInstanceType
- EcsSystemDiskCategory
- EcsSystemDiskSize
- EcsPassword
Label:
default: ECS
- Parameters:
- BucketName
- BucketDeletionForce
Label:
default: OSS
- Parameters:
- UserName
- UserPassword
Label:
default: RAM
TemplateTags:
- acs:solution:生命科学:BCS三代基因测序数据组装
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