SMRT Link Services
SMRT Link Services
Release 5.1.0 Pacific Biosciences
Apr 26, 2018
Contents
1 Introduction
1
2 SMRT Link System Architecture High Level Overview
3
2.1 ServiceJob . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.1.1 Import DataSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1.2 Fasta Reference Convert and Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1.3 "Analysis" or "pbsmrtpipe" Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1.4 Other Job Types Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.5 ServiceJob Data Model and Polymorphism . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 DataStore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.3 SMRT Link Importing of DataStoreFile(s) from a DataStore . . . . . . . . . . . . . . . . . . . . . . 6
2.3.1 PacBio DataSet Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.3.2 PacBio Report Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.3.3 Accessing Report(s) from SMRT Link Analysis . . . . . . . . . . . . . . . . . . . . . . . . 7
2.4 SMRT Link Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3 Tools
9
3.1 Commandline Interaction with SMRT Link Services . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.1.1 Checking the Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.1.2 Importing a DataSet into SMRT Link Server . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.1.3 Submit an Resequencing Analysis Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.1.4 Resubmitting an Analysis Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.1.5 Importing/Converting a RSII movie into SMRT Link . . . . . . . . . . . . . . . . . . . . . 10
3.1.6 Querying Job History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.1.7 Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.2 Conversion and Other Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.2.1 Fasta to ReferenceSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.2.2 Convert RSII movie metadata XML to HdfSubreadSet XML . . . . . . . . . . . . . . . . . 11
4 SMRT Link Analysis Services Config
13
4.1 Common Analysis Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
4.2 SMRT Link Bundle External Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.3 Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
5 PacBio Data Bundle Model and Services
15
5.1 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
5.2 Example PacBio Data Bundle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
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5.3 PacBio Data Bundle Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 5.4 SMRT Bundle Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 5.5 Servers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 5.6 Legacy API . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 5.7 Building a Stand Alone Chemistry Update Bundle Server . . . . . . . . . . . . . . . . . . . . . . . 18 5.8 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 5.9 Details of the Root Bundle Dir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 5.10 Building and Starting up the Chemistry Bundle Upgrade Server . . . . . . . . . . . . . . . . . . . . 19 5.11 Getting a List of PacBio Data Bundles from SMRT Link Server . . . . . . . . . . . . . . . . . . . . 19 5.12 Bundles Stored within the SL System install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
5.12.1 Chemistry Data Bundle Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 5.13 SMRT Link PartNumbers and Automation Constraints WebService . . . . . . . . . . . . . . . . . . 20 5.14 SMRT Link Periodic Checking for Chemistry Data Bundle Upgrades . . . . . . . . . . . . . . . . . 20
6 SMRT Link Analysis Services API
21
7 Eve SMRT Server for Events and Tech Support File Uploads
23
7.1 General Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
7.2 System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
7.3 Building, Configuring and Starting up Eve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
7.4 Build . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
7.5 Start the Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
7.6 Eve and SMRT Link Server Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
7.7 Tech Support TGZ Bundle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
7.8 Eve WebServices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
7.9 Events/Messages Generated Within SMRT Link Analysis Service . . . . . . . . . . . . . . . . . . . 26
7.9.1 How Messages are sent out of SMRT Link to External Server . . . . . . . . . . . . . . . . . 27
8 Logging configuration
29
8.1 Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
8.2 Command-Line Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
9 PacBio Update Server
33
9.1 Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
9.2 Packaging Chemistry Update Bundle Server Build . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
9.3 Install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
9.4 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
9.5 Systemd service definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
9.6 Upgrade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
9.7 Automated build and deploy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
10 SMRT Link Services Common Tasks And Workflows
37
10.1 How to get the reports for SMRT Link Job By Id . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
10.1.1 How to get the SMRT Link reports for dataset by UUID . . . . . . . . . . . . . . . . . . . 38
10.1.2 How to get QC reports for a particular SMRT Link Run . . . . . . . . . . . . . . . . . . . . 39
10.1.3 How to get QC reports for a particular Collection . . . . . . . . . . . . . . . . . . . . . . . 40
10.1.4 How to get recent Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
10.1.5 How to setup a Run in Run Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
10.1.6 How to monitor progress of a SMRT Link Run . . . . . . . . . . . . . . . . . . . . . . . . 42
10.1.7 How to capture Run level summary metrics . . . . . . . . . . . . . . . . . . . . . . . . . . 44
10.1.8 How to setup a job on a particular Collection . . . . . . . . . . . . . . . . . . . . . . . . . 44
10.1.9 How to delete a SMRT Link Job . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
10.1.10 How to setup a SMRT Link Analysis Job for a specific Pipeline . . . . . . . . . . . . . . . . 49
10.1.11 Querying Job History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
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11 Disclaimer
53
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