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1. CLC Bioinformatics Database User manual Manual for CLC Bioinformatics Database 3 7 Windows Mac OS X and Linux April 12 2013 This software is for research purposes only CLC bio Finlandsgade 10 12 DK 8200 Aarhus N gt Denmark T LLL bio Contents 1 Introduction 6 1 1 System requirements 1 2 ee ine R e r amp maw ea hee toe eee ee Ea ewe ea ee wee ee 4 6 Installation 8 2 1 Quick installation guide ee aan be GREE PRE ee Be GRE RADE ee eS 8 2 2 Installing the database 4 de ewe Ee a ee OEE ew Ee eR EE a 8 2 2 1 Download and install a Database Management System 8 2 2 2 Create anew database and user role 2 ee ee ee ee a 9 223 nit alz Wie datapase aa i aa es ee oe ee R R ee I R we N 9 2 3 Installing and running the Server lt 2s22es ge 6 ebb eee nde de Bee 10 2 3 1 Installing the Server software 2 0 eee ee ee a 11 2 4 Silent installation coca aooo a 12 2 5 Upgrading an existing installation aoao oaoa a a a 13 2 5 1 Upgrading major versions 6 iow aa oa e ee hea oe a ee ee Ee we 13 2 6 Allowing access through your firewall 1 ee a 13 2 f Downloading alicense 1 we ee ee a 13 2 1 Windows license download 24 ew ee ee ew ew ew ee ew Se we 14 2Ave Mac OS license download oi i o eee wee CROSS Ee EES SG 14 Stem LINUX Cense dOwNIOaQ s i i esa aramak ice ance buaa se amp 14 2 8 Starting and stopping the server ooo a a a 15 2 8 1 Microsoft Windows aoaaa a eo
2. the built in system is used all the functionality described below is relevant if an external system is used for managing users and groups the menus below will be disabled 4 3 User authentication using the Workbench Users and groups can also be managed through the Workbench note that you need to set up the authentication mechanism as described in section 4 2 File Manage Users and Groups This will display the dialog shown in figure 4 5 Users Membership Groups l All Users clcuser test_admin test_readonly test_user cp Add Hep vok Figure 4 5 Managing users 4 3 1 Managing users through the Workbench Click the Add button to create a new user Enter the name of the user and enter a password You will be asked to re type the password If you wish to change the password at a later time select the user in the list and click Change password 521 To delete a user select the user in the list and click Delete 4 3 2 Managing groups through the Workbench Access rights are granted to groups not users so a user has to be a member of one or more groups to get access to the data location Here you can see how to add and remove groups and next you will see how to add users to a group Adding and removing groups is done in the Groups tab see figure 4 6 To create a new group click the Add button and enter the name of the group To delete a group select the group in
3. you will need to right click on the installer file icon and choose to Run as administrator e For the Linux based installation script you would normally wish to install to a central location which will involve running the installation script as an administrative user either by logging in as one or by prefacing the command with sudo Please check that the installation script has executable permissions before trying to execute it AOP Enter Password A Please enter your password You must be a member of the Administrator group OK L Cancel Figure 2 2 Enter your password Next you will be asked where to install the server 2 3 If you do not have a particular reason to change this simply leave it at the default setting The chosen directory will be referred to as the server installation directory throughout the rest of this manual AAA Setup CLC Genomics Server 1 0 Select Destination Directory AT Where should CLC Genomics Server be installed f Select the folder where you would like CLC Genomics Server to be installed then click Next Destination directory Applications CLCGenomicsServer L Browse Required disk space 108 1 MB Free disk space 19 835 MB L lt Back d L Next gt d Cancel d Figure 2 3 Choose where to install the server CHAPTER 2 INSTALLATION 12 The installer allows you to specify the maximum amount of memory the CLC Server will be able to utilize 2 4 The ra
4. you will often be asked for additional information about the server set up etc In this case you can easily send the necessary information by submitting a bug report Log in to the web interface of the server as administrator report a bug at the top right corner Enter relevant information with as much detail as possible Submit Bug Report to CLC bio You can see the bug report dialog in 6 2 The bug report includes the following information e Log files e A subset of the audit log showing the last events that happened on the server e Configuration files of the server configuration In a job node set up you can include all this information from the job nodes as well by checking the Include comprehensive job node info checkbox in the Advanced part of the dialog 33 CHAPTER 6 APPENDIX 34 rsetup diagnostics Generate diagnostics report ff Master and job nodes version match sf Job distribution J File system locations consistency ff Job nodes configuration integrity J Job nodes plugin integrity ff Index server status ff File system locations permissions J Grid setup status Close Figure 6 1 Check system Failed elements will be marked with a red X If you have not configured your Server to submit jobs to a local Grid system or if you have and your setup is configured correctly you will see a green checkmark beside the Grid setup status item in the diagnostic report Export data C2 Import data
5. 1 7 Please refer to your operating system documentation if you require further information about setting up services on your system 2 9 Installing relevant plug ins in the Workbench In order to use the CLC Bioinformatics Database from a CLC Workbench you need to install the CLC Workbench Client Plug in in the Workbench This plug in is needed for logging onto the server and accessing data from the server data locations Plug ins are installed using the Plug ins and Resources Managert which can be accessed via the menu in the Workbench Help Plug ins and Resources 221 or via the Plug ins button on the Toolbar From within the Plug ins and Resources Manager choose the Download Plug ins tab and click on the CLC Workbench Client Plugin Then click in the button labelled Download and Install If you are working on a system not connected to the network then you can also install the plug in by downloading the cpa file from the plugins page of our website Hebe T Www Cleo con L e LAE DT Then start up the Plug in manager within the Workbench and click on the button at the bottom of the Plug in manager labelled Install from File You need to restart the Workbench before the plug in is ready for use Note that if you want users to be able to use External applications see chapter 771 on the server there is a separate plug in CLC External Applications Plug in that needs to be installed in the Workbench the same way as describ
6. ClipBook Enables ClipBook Viewer to store By COM Event System Supports System Event Notificati Sy COM System Application Manages the configuration and tr 4 Computer Browser Maintains an updated list of comp Bs Cryptographic Services Provides three management serv SRy DCOM Server Process Launcher Provides launch Functionality for b Extended Standard SRA DHCP Client Manages network configuration b lt Status Started Started Started Started Started Started A Figure 2 7 Stopping and restarting the server on Windows by clicking the blue links 2 8 2 Mac OS X On Mac OS X the server can be started and stopped from the command line Open a terminal and navigate to the CLC Server installation directory Once there the server can be controlled with the following commands CHAPTER 2 INSTALLATION 16 To start the server run the command sudo CLCBioinformaticsDatabase start To stop the server run the command sudo CLCBioinformaticsDatabase stop To view the current status of the server run the command sudo CLCBioinformaticsDatabase status You will need to set this up as a service if you wish it to be run that way Please refer to your operating system documentation if you are not sure how to do this 2 8 3 Linux You can start and stop the Genomics Server from the command line You can also run it as a service Command Line Open a terminal and navigate to the CL
7. Installing the database 2 2 1 Download and install a Database Management System If you do not already have an existing installation of a Database Management System DBMS you will have to download and install one The CLC Bioinformatics Database can be used with a 8 CHAPTER 2 INSTALLATION 9 number of different DMBS implementation Choosing the right one for you and your organization depends on many factors such as price performance scalability security platform support etc Information about the supported solutions are available on the links below MySQL http dev mysql com downloads PostgreSQL http www postgresql org Microsoft SQL Server http www microsoft com SQL e Oracle http www oracle com If you have further questions about the installation of the DBMS please contact support clcbio com See section 6 2 for guidance on special configurations for the DBMS 2 2 2 Create a new database and user role Once your DBMS is installed and running you will need to create a database for containing your CLC data We also recommend that you create a special database user sometimes called a database role for accessing this database Consult the documentation of your DBMS for information about creating databases and managing users roles 2 2 5 Initialize the database Before you can connect to your database from a CLC Workbench or Server it must be initialized The initialization creates the required tables
8. Sequence Text Download 4 Upload Main configuration Authentication Y change root password Current password eeee New password 6666666 verify password eeeee sel J Change Root Password P Authentication mechanism Figure 4 1 We recommend changing the root password The verification of the root password is shown with the green checkmark 4 2 User authentication using the web interface When the server is installed you can log in using the default root password username root password default Note that if you are going to use job nodes it makes sense to set this up first before changing the authentication mechanism and root password see section 771 23 CHAPTER 4 MANAGING USERS AND GROUPS 24 Once logged in you can specify how the general user authentication should be done Admin 73 Authentication Authentication mechanism This will reveal the three different modes of authentication as shown in figure 4 2 3f Element Info CD History Sequence Text F Download 4 Upload 5 Main configuration Authentication P change root password Y authentication mechanism Built in authentication Ov pap directory O active directory save Configuration 5 Job nodes gt Queue User statistics lt Plugins Audit log Figure 4 2 Three modes of user authentication The options are e Built in authentication This option will enable you to set up user authentication using th
9. can specify which groups should have access by clicking the Edit Permissions button A dialog will appear like that in figure 5 4 If you choose Only authorized users from selected groups you will be offered a list of groups that you can select or de select to give or take away access to that functionality ermissions for Annotate and Merge Counts Listing and execution of Annotate and Merge Counts is granted to All authorized users Only authorized users from selected groups Figure 5 4 Setting permissions for an alorithm The default configuration is that all users have access to everything Chapter 6 Appendix 6 1 Troubleshooting If there are problems regarding the installation and configuration of the server please contact Support clcbio com 6 1 1 Check set up In order to check that your server has been set up correctly you can run the Check set up tool Log in on the web interface of the server as an administrator and click the Check Set up link at the upper right corner This will show a dialog where you click Generate Diagnostics Report This will show a list of test that are performed on the system as shown in figure 6 1 If any of the tests fail it will be shown in the list You can expand each of the tests to display more information about what the test is checking and information about the error if it fails 6 1 2 Bug reporting When contacting support clcbio com regarding problems on the server
10. on the system you have installed the software on You can manually change the number contained in the relevant line of the vmoptions file for your CLC Bioinformatics Database if you wish to raise or lower the amount of RAM allocated to the Java Virtual Machine 3 5 Limiting the number of cpus available for use A number of the algorithms in the CLC Bioinformatics Database will in the case of large jobs use all the cores available on your system to make the analysis as fast as possible If you wish CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 22 to restrict this to a predefined number of cores this can be done with a properties file Create a text file called cou properties and save it in the settings folder under the CLC Bioinformatics Database installation directory The cpu properties file should include one line like this maxcores 1 Restart the CLC Bioinformatics Database if you create or change this file for these settings to take effect Instead of 1 you write the maximum number of cores that the CLC Bioinformatics Database is allowed to use Please note that this is not a guarantee that the CLC Bioinformatics Database will never use more cores than specified but that will be for very brief and infrequent peaks and should not affect performance of other applications running on your system You can download a sample cpu properties file athttp clcbio com files deployment cpu properties 3 6 Other configurations
11. oom ew we 15 Ea E E ea aea eaea be os 15 e A ck ee a aaa a eee a 16 2 9 Installing relevant plug ins in the Workbench n nononono oaoa oa a a 17 CONTENTS 3 Configuring and administering the server 5 3 1 Logging into the administrative interface 0 2 00 ee eee 3 2 Adding locations for saving data 0 0 02 e a ee ee es fe 3 4 29 3 6 3 2 1 3 2 2 K ae Adding a database location io kaw be He ee aw ee we ee Adding a file system location 1 eee a ee Important points about the CLC Server data in the file system locations File locations for job node set upS a a a ee ee a POOUNCINS TING INON ew ee ee oe ee yE changing the listening POTE 0 Sea Be eee eee eee ee Setting the amount of memory available forthe JVM Limiting the number of cpus available for use 0 2 00 ees her CONTECUAUONS s s s resa ee eh ae eee a ee ee Be Ge et es 3 6 1 3 6 2 30 3 ALIF SCUO eee be SEEGER Eee Ree RB eee eee EG PUGH IOE SEUWINES o a eee ae ee ee Pee eee Ee ee eee ee Deployment of server information to CLC Workbenches Managing users and groups 4 1 Logging in the first time root password 1 e a es 4 2 User authentication using the web interface 2 508258 4 3 4 2 1 4 2 2 Managing users using the web interface n nonon 2005 Managing groups using the web interface 1 oaoa oaoa e a e User authentication using th
12. ra Admin Submit or download bug report Submit bug report to CLC bio or download locally Thank you for taking your time to do this Your feedback is important to us Your email address Message to CLC bio Cancel Download Bug Report Submit Bug Report to CLC bio Figure 6 2 Submitting a bug report to CLC bio lf the server does not have access to the internet you can Download bug report This will create a zip file containing all the information and you can pass that on to CLC bio support If the server has access to the internet you can Submit Bug Report to CLC bio Note that the process of gathering the information for the bug report can take a while especially for job node set ups If a Workbench user experiences a server related error it is also possible to submit a bug report from the Workbench error dialog This report will include the same archive as when submitting a bug report from the web interface All data sent to support clcbio com is treated confidentially CHAPTER 6 APPENDIX 35 No password information is included in the bug report 6 2 Database configurations 6 2 1 Configurations for MySQL For MySQL we recommend basing your configuration on the example configuration file my large cnf which is included in the MySQL distribution In addition the following changes should be made The max_allowed_packet should be increased to allow transferring large binary objects to an from the database This i
13. to clean up the permission structure of the subfolders It should be applied with caution since it can potentially destroy valuable permission settings in the subfolder structure Permissions on the recycle bin The recycle bin is conceptually a folder like any else It is special in the sense that all users must have write access otherwise they will not be able to delete anything Because there is one recycle bin for the data from all users you should be careful granting everybody read access to the recycle bin since they will then be able to see the data deleted by other users We recommend only granting read access to administrators Only administrators are allowed to empty the recycle bin 5 1 2 Technical notes about permissions and security All data stored in CLC Bioinformatics Database file system locations are owned by the user that runs the CLC Bioinformatics Database process Changing the ownership of the files using standard system tools is not recommended and will usually lead to serious problems with data indexing and hamper your work on the CLC Bioinformatics Database One implication of the above ownership setup is that by default i e without permissions enabled all users logging into the CLC Bioinformatics Database are able to access all data within that file system location and write data to that file system locations All files created within such a file system location are then also accessible to all users of the CLC B
14. 3 6 1 HTTP settings Under the Admin Ga tab click Configuration and you will be able to specify HTTP settings Here you can set the time out for the user HTTP session and the maximum upload size when uploading files through the web interface 3 6 2 Audit log settings The audit log records all the actions performed in the web interface and through the Workbenches Note that data management operations copying deleting and adding files done through the Workbench are not recorded 3 6 3 Deployment of server information to CLC Workbenches See the Deployment manual at http www clcbio com usermanuals for information on pre configuring the server log in information when Workbench users log in for the first time Chapter 4 Managing users and groups 4 1 Logging in the first time root password When the server is installed you will be able to log in via the web interface using the following credentials e User name root e Password default Once logged in you should as a minimum set up user authentication see section 4 2 and data locations see section 3 2 before you can start using the server For security reasons you should change the root password see figure 4 1 Admin Authentication Change root password Note that if you are going to use job nodes it makes sense to set these up before changing the authentication mechanism and root password see section 771 amp Element Info CD History
15. C Server installation directory Once there the server can be controlled with the following commands To start the server run the command CLCBioinformaticsDatabase start To stop the server run the command CLCBioinformaticsDatabase stop To view the current status of the server run the command CLCBioinformaticsDatabase status You can run these commands as any user either directly on the command or by prefacing the commands with sudo e g sudo lt username 2 CICBI6intormattesbDatabace Status Please note To run the Genomics Server as a non root user you should first ensure that the files under your CLC Bioinformatics Database installation directory have the appropriate permissions The easiest way to do this is to recursively change the ownership of all the files in that directory to the user that will run the CLC Bioinformatics Database process As a service On installation a link is created in etc init d to the CLCBioinformaticsDatabase script At this point you need to configure it as a service For example on Red Hat systems e service clcserver startupscript start We provide an example wrapper script for running the CLC Bioinformatics Database process You may find this convenient if you plan to run the process as a user other than the root user The script is called clcserver startupscript and can be found under the conf directory of the CLC Bioinformatics Database installation area CHAPTER 2 INSTALLATION
16. Configuration Figure 3 2 File system location settings In this dialog enter the path to the folder you want to use for storing the data The path should point to an existing folder on the server machine and the user running the server process needs to have read and write access to the folder This is usually a dedicated user or it may be the system s root user if you have not created a dedicated user for this purpose The file location s configured on the server will be accessible to those working using CLC Workbenches after they log into the server via their Workbench Once you have pressed Save Configuration learn more about rebuilding the index in section 3 2 3 this location will be added and it should now appear in the Navigation Area in the left hand side of the window By default it will also appear in the Workbench on next login You can use the checkbox next to the location to indicate whether it should be visible to your users or not CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 20 You can choose whether access control should be switched on and off Please see section 5 1 for more information about enabling and setting permissions on CLC Bioinformatics Database data folders Note that pressing Remove Location will only remove the location from this list it will not delete the folder from your system or affect any data already stored in this folder The data will be accessible again simply by adding the folder as
17. Locality Aarhus N State N A Country DK Issuer Common Name localhost Organizational Unit Enterprise Organization CLC Bio Locality Aarhus N State N A Country DK Fingerprints SHA 1 Fingerprint A5 F6 8D C4 F6 E9 36 14 AE 9 SHA 256 Fingerprint 4B B5 OB 04 3C F6 Fa C 6 8 3A B 8 6 B 44 DO BA 83 B 9B 9C F9 Al 10 F1 5D EA DD 9B 92 9435 48 AF F6 98 87 OF Validity Period Valid From Sep 1 2011 Valid To Aug 31 2012 Do you want to trust this certificate no Figure 6 3 A warning is shown when the certificate is not signed by a recognized CA g i Idle Connected to localhostlocaldomain running CLC Genomics Server 3 2 1 as user root Connection is encrypted lick to view server s certificate Figure 6 4 Showing details on the server connection by placing the mouse on the globe 6 3 3 Enabling redirection from non ssl port to ssl enabled port If SSL is to be mandatory it is possible to get the non ssl port 7777 to forward to the ssl port 8443 rather than closing down the non ssl port This is done by adding the following section to the conf web xml file lt security constraint gt lt display name gt Security Constraint lt display name gt lt web resource collection gt lt web resource name gt SSL restricted Area lt web resource name gt lt url pattern gt lt url pattern gt lt web resource collection gt lt user data constraint gt lt tran
18. a new location again Important points about the CLC Server data in the file system locations Any file system locations added here should be folders dedicated for use by the CLC Bioinformatics Database Such areas should be directly accessed only by the CLC Bioinformatics Database In other words files should not be moved into these folders or their subfolders manually for example using your standard operating system s command tools drag and drop and so on All the data stored in this areas will be in clc format and will be owned by the user that runs the CLC Bioinformatics Database process File locations for job node set ups When you have a job node set up all the job node computers need to have access to the same data location folder This is because the job nodes will write files directly to the folder rather than passing through the master node which would be a bottleneck for big jobs Furthermore the user running the server must be the same for all the job nodes and it needs to act as the same user when accessing the folder no matter whether it is a job node or a master node The data location should be added after the job nodes have been configured and attached to the master node In this way all the job nodes will inherit the configurations made on the master node One relatively common problem faced in this regard is root squashing which often needs to be disabled because it prevents the servers from writing and accessing t
19. ation mode which is activated by the q parameter when running the installer from a command line e g CLCGenomicsServer_3_0 exe q On Windows if you wish to have console output console can be appended as the second parameter this is only needed when running on Windows where there is no output per default CLCGenomicsServer_3_0 exe q console You can also in silent mode define a different installation directory dir CLCGenomicsServer_3_0 exe q console dir c bioinformatics clc Note Both the console and the dir options only work when the installer is run in silent CHAPTER 2 INSTALLATION 13 mode The q and the console options work for the Uninstall program as well 2 5 Upgrading an existing installation Upgrading an existing installation is very simple For a single Genomics Server the steps we recommend are e Make sure that nobody is using the server see section 4 4 A standard procedure would be to give users advance notice that the system will be unavailable for maintenance e Install the server in the same installation directory as the one already installed All settings will be maintained If you have a CLC job node setup you will also need to upgrade the CLC Bioinformatics Database software on each job node Upgrading the software itself on each node is all you need to do Configurations and plug ins for job nodes are pushed to them by the master node 2 5 1 Upgrading major versions Once you have p
20. e s User statistics Number of users logged in 1 Number of logins 2 User Sessions a d Gi II aiaa Refresh Statistics 9 Audit log Figure 4 8 The user statistics user names have been blurred You can also log users off by expanding the user sessions on the sign and the click Invalidate Session This will open a confirmation dialog where you can also write a message to the user that will be displayed either in the Workbench or the browser Chapter 5 Access privileges and permissions The CLC Bioinformatics Database allows server administrators to control access to the server on several levels e Access to the data in the server s data locations This is typically to allow groups of users to store data that cannot be accessed by other users or to establish reference data sources that are read only for most users e Access to running jobs on the server Particular groups of users can be restricted to running only particular types of jobs on the server e Access to the import export directories The server administrator can give users access to browsing designated directories on the server file system Thus it can be desirable to restrict this access to certain groups of users for security reasons The following sections describe each of these levels 5 1 Controlling access to data The CLC Bioinformatics Database uses folders as the basic unit for controlling access to data and access is granted or d
21. e Workbench 2 6 2 eee ee ee ee we ee eS 4 3 1 4 3 2 4 3 3 Managing users through the Workbench aaao a a a Managing groups through the Workbench 4 Adding users toa group 2 a a a a 4 4 User statistics 0 0 08 eee ee ee ee kk ee a Access privileges and permissions 5 1 Controlling access to data 2 64 chs tee ree bee ewe a aL ILL Setting permissions on a folder a aooo a a ee Permissions on the recycle bin nononono a ee Technical notes about permissions and security aoao aoao aooaa 5 2 Global permissions ao aooaa a a a a a es bbe ee hE es 18 18 18 18 19 20 20 20 21 21 21 22 22 22 22 23 23 23 24 25 26 26 26 2 2 CONTENTS 6 Appendix 6 1 Troubleshooting 2 3 ee ee DRS Ge ee HR RK ee we 6 1 1 6 1 2 Check set up ow dw ewe a ew ee ee ee we ee BUS TOTS s s a saame ap EERE Rw Be owe oY 6 2 Database configurations osoasa ee open Configurations for MySQL 1 a a a a 6 3 SoLand SHC DUON 4 amp gunk wee ue ee ww R ee K we eS ee one mel 6 3 2 6 3 3 6 3 4 Bibliography Index Enabling SSL on the server oaos a Creating a PKCS12 keystore file 02 epee eae Logging in using SSL from the Workbench Enabling redirection from non ssl port to ssl enabled port Logging in using SSL from the CLC Server Command Line Tools 33 33 33 33 35 35 35 35 36 36 or 38 39 39 Chapter 1 Introd
22. e server s built in user management system This means that you create users set passwords assign users to groups and manage groups using the web interface see section 4 2 1 or using the Workbench see section 4 3 1 All the user information is stored on the server and is not accessible from other systems e LDAP directory This option will allow you to use an existing LDAP directory This means that all information needed during authentication and group memberships is retrieved from the LDAP directory If needed the LDAP integration can use Kerberos GSSAPI e Active directory This option will allow you to use an existing Active directory which is Microsoft s LDAP counterpart This means that all information needed during authentication and group memberships is retrieved from the Active directory For the two last options a settings panel will be revealed when the option is chosen allowing you to specify the details of the integration Note that membership of an administrative group is used to control which users can access the admin part of the web interface These users will also be able to set permissions on folders see section 5 For the built in authentication method this means adding particular users to the built in admin group For Active Directory or LDAP this means designating a group in the box labeled Admin group name and adding any users who should be administrators of the CLC Server to this group 4 2 1 Managing user
23. ed above In order to install plug ins on many systems the Workbench must be run in administrator mode On Windows Vista and Windows 7 you can do this by right clicking the program shortcut and choosing Run as Administrator Chapter 3 Configuring and administering the server 3 1 Logging into the administrative interface Once the server is running you can log into its administrative interface via a web browser Most configuration occurs via this interface Simply type the host name of the server machine you have installed the CLC Bioinformatics Database software on followed by the port it is listening on Unless you change it the port number is 7 777 An example would be http cloecomputer 7777 The default administive user credentials are username root password default Use these details the first time you log in 3 2 Adding locations for saving data Before you can use the server for doing analyses you will need to add one or more locations for storing your data The locations can either be simple pointers to a folder on the file system or based on a CLC Bioinformatics Database To set up a location open a web browser and navigate to the CLC Server web interface Once logged in go to the Admin tab and unfold the Main configuration section There are two headings relating to CLC data storage Database locations and File system locations 3 2 1 Adding a database location Before adding a database location you n
24. eed to set up the database This is described in section ae Under the Database locations heading click the Add New Database Location button to add a new database location see figure 3 2 Enter the required information about host port and type of database The user name and password refers to the user role on your Database Management System DBMS see section 18 CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 19 Add new database location Y cledb MySql cledb Database type MySql M Port 3306 Database name clcdb Username cledb Password 66666 Rebuild index when adding location recommended Save configuration Cancel Figure 3 1 Database location settings 2 2 Note that there are two version of Oracle in the list One is the traditional using SID style e g jdbc oracle thin HOST PORT SID and the other is using thin style service name e g jdbc oracle thin HOST PORT SERVICE Click the Save Configuration button to perform the changes The added database location should now appear in the Navigation Area in the left hand side of the window 3 2 2 Adding a file system location Under the File system locations heading click the Add New File Location button to add a new file system location see figure 3 2 a _j 1 Mor fila RA as h TAR x AU U el E a 1817 Path mnt data clce_data Permissions enabled Rebuild index when adding location recommended Save
25. enied to groups of users On any folder within a location you can grant two kinds of access to a group Read access his will make it possible for the users of the group to see the elements in this folder to open them and to copy them Access can be through any route for example browsing in the Navigation Area searching or clicking originates from in the History Ci of e g an alignment Write access Changes to an element can be saved Save Eh and new elements and subfolders can be created For a user to be able to access a folder there has to be at least read access to all the top folders In the example shown in figure 5 1 to access the Sequences folder the user must have at least read access to both the Example Data and Protein folders 29 CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 30 ct a Example Data E Cloning vectors EJ Extra L la Nucleotide ka Protein E J 3D structures HJ More data Ea Sequences os 1A29 HUMAN a r CAA24102 p r CAA32220 i fe NP_058652 Fh Ps04o p r P6s053 po lth P6s063 lth P6225 ov LPM DG Z 25 Figure 3 1 A folder hierarchy on the server z H B F i jj i Oe T However you can grant read access to the Example Data and Protein folders and only grant write access to the Sequences folder Permissions on file system locations must be explicitly enabled if they are desired see section 3 2 2 Please see 5 1 2 for further details about the system behaviour
26. erformed the steps mentioned above there are a few extra details whenever the release is more than a bug fix upgrade e g a bug fix release would be going from version 1 0 to 1 0 1 First make sure all client users are aware that they must upgrade their Workbench and server connection plug in For major versions e g going from 1 X to 2 0 a new license needs to be downloaded see section 2 and the server restarted 2 6 Allowing access through your firewall By default the server listens for TCP connections on port 7777 See section 3 3 for info about changing this If you are running a firewall on your server system you will have to allow incoming TCP connections on this port before your clients can contact the server from a Workbench or web browser Consult the documentation of your firewall for information on how to do this Besides the public port described above the server also uses an internal port on 7776 There is no need to allow incoming connections from client machines to this port 2 7 Downloading a license The CLC Bioinformatics Database will look for licenses in the licenses folder This means that all license files should be located in this folder Check the platform specific instructions below to see how to download a license file CHAPTER 2 INSTALLATION 14 2 7 1 Windows license download License files are downloaded using the downloadlicense command script To run the script right click on the file and ch
27. for holding objects and prepares an index used for searching Initialization is performed with the CLC Bioinformatics Database Tool figure 2 1 e Install the CLC Bioinformatics Database Tool on a client machine and start the program e Fill in the fields with the required information Hostname The fully qualified hostname of the server running the database NOTE The same hostname must be used every time you connect to the database Port The TCP IP listening port on the database server Database name The name of the database you created in the previous section Username the name of the user role you created in the previous section Password the password for the user role e To re initializing an existing CLC database you must check the Delete Existing checkbox NOTE ANY DATA ALREADY STORED IN THE CLC DATABASE WILL BE DELETED e Click the Initialize Database button to start the process While the program is working the progress bar will show the status and the transcript will show a log of actions events and problems If anything goes wrong please consult the transcript for CHAPTER 2 INSTALLATION 10 atap dh CLC Bioinformatics Database Database Type MySql HH Hostname host example com Port 3306 Database name icledb Username cledbuser C Delete existing CLC tables in the database Initialize Database a bh ae aie eter Figure 2 1 The CLC Bioinformatics Database tool m
28. he files as the same user read more about this at http nfs sourceforge net faq_bll You can read further about job node setups in section 3 2 3 Rebuilding the index The server maintains an index of all the elements in the data locations The index is used when searching for data For all locations you can choose to Rebuild Index This should be done only when a new location is added or if you experience problems while searching e g something is missing from the search results This operation can take a long time depending on how much data is stored in this location lf you move the server from one computer to another you need to move the index as well Alternatively you can re build the index on the new server this is the default option when you add a location If the rebuild index operation takes too long and you would prefer to move the old index simply copy the folder called searchindex from the old server installation folder to the new server The status of the index server can be seen in the User Statistics pane showing information on where the index server resides and the number of locations currently being serviced CHAPTER 3 CONFIGURING AND ADMINISTERING THE SERVER 21 3 3 Changing the listening port The default listening port for the CLC Server is 7777 This has been chosen to minimize the risk of collisions with existing web servers using the more familiar ports 80 and 8080 If you would like to have the server li
29. if permission are not enabled and configured If permissions are enabled on a file system location then by default no groups have read or write access to any area under this location until permissions are configured Only the CLC Bioinformatics Database root user will have access to the data held in the server at this point In other words you must set permissions on folders in this file system location before any users will be able to read from or write to it 5 1 1 Setting permissions on a folder This step is done from within a CLC Workbench Start up a copy of a Workbench that has the CLC Workbench Client plugin installed From within the Workbench go to the File menu and choose the item CLC Server Login Log into the CLC Server as an administrative user You can then set permissions on folders in your database if you have one or on folders within file system locations that have had permissions enabled right click the folder 71 Permissions This will open the dialog shown in figure 5 2 Set the relevant permissions for each of the groups and click OK If you wish to apply the permissions recursively that is to all subfolders check Apply to all subfolders in the dialog shown in figure 5 2 Note that this operation is only relevant if you wish CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 31 Le Permissions Read permission Write permission Apply to all subfolders Xora Figure 5 2 Setting permissions on a folder
30. ioinformatics Database Group permissions on file system locations is an additional layer within the CLC Bioinformatics Database and is not part of your operating system s permission system This means that enabling permissions and setting access restrictions on CLC file system locations only affects users accessing data through CLC tools e g using a Workbench the CLC Command Line Tools the CLC Bioinformatics Database web interface or the Server API If users have direct access to the data using for example general system tools the permissions set on the data in CLC Bioinformatics Database has no effect CHAPTER 5 ACCESS PRIVILEGES AND PERMISSIONS 32 5 2 Global permissions In the server web interface in the Admin tab you can set global permissions for the CLC Bioinformatics Database as shown in figure 5 3 f Element Info LD History Sequence Text Export data E Import data s Main configuration Authentication Global permissions Algorithms External applications core tasks gt Import export directories CS Job distribution Figure 5 3 Global permissions Permissions can be set for e Algorithms All the algorithms running on the server are listed here External applications All the external applications configurations are listed here Core tasks These are general import export and maintenance tasks import export directories Permissions can be set for each of the directories defined You
31. kcs12 keystore file it can be put into one by combining the private key and the signed certificate obtained from the CA by using openssl openssl pkcs12 export out keystore pkcs12 inkey private key in certificate crt name tomcat This will take the private key from the file private key and the signed certificate from certificate crt and generate a pkcs12 store in the keystore pkcs12 file 6 3 2 Logging in using SSL from the Workbench When the Workbench connects to the CLC Bioinformatics Database it automatically detects if Secure Socket Layer SSL should be used or not If SSL is detected the server s certificate will be verified and a warning is displayed if the certificate is not signed by a recognized Certificate Authority CA as shown in figure 6 3 When such an unknown certificate has been accepted once the warning will not appear again It is necessary to log in again once the certificate has been accepted When logged into a server information about the connection can be viewed by hovering the connection icon on the status panel as shown in figure 6 4 The icon is gray when the user is not logged in and a pad lock is overlayed when the connection is encrypted via SSL CHAPTER 6 APPENDIX ar Untrusted Certificate The server localhost presented an unknown certificate with the following attributes Subject Common Name localhost Alternative names N A Organizational Unit Enterprise Organization CLC Bio
32. nge of choice depends on the amount of memory installed on your system and on the type of machine used On 32 bit machines you will not be able to utilize more than 2 GB of memory on 64 bit machines there is no such limit If you do not have a reason to change this value you should simply leave it at the default setting E Setup CLC Genomics Server 3 6 SU gt en Configure memory limit Select the amount of memory available to the CLC Server L 3956 System Memory 7912 MB Maximum value 7912 MB The maximum possible value depends on your operating system amount of system memory and type of computer 32 bit or 64 bit ced Figure 2 4 Choose the maximum amount of memory used by the server If you are installing the server on a Windows system you will be able to choose if the service is started manually or automatically by the system The installer will now extract the necessary files On a Windows system if you have chosen that the service should be started automatically the service should also start running at this point Please note that if you do not already have a license file installed then the CLC Bioinformatics Database process will be running in a limited capacity at this point Downloading a license is described in section 2 7 Information on stopping and starting the CLC Bioinformatics Database service is provided in section 2 8 2 4 Silent installation The installer also has a silent install
33. oose Run as administrator This will present a window as shown in figure 2 5 Gee C Windows System32 cmd exe H cat a a A L Hit CLO bio license download utilit BEINEN NIEH aa aa Hostname Host IDCs Please enter Cor copy paste your license Order ID and press return gt Figure 2 5 Download a Ona based on the Order ID Paste the Order ID supplied by CLC bio right click to Paste and press Enter Please contact Support clcbio com if you have not received an Order ID Note that if you are upgrading an existing license file this needs to be deleted from the licenses folder When you run the downloadlicense command script it will create a new license file Restart the server for the new license to take effect see how to restart the server in section 2 8 1 2 7 2 Mac OS license download License files are downloaded using the downloadlicense command script To run the script double click on the file This will present a window as shown in figure 2 6 Paste the Order ID supplied by CLC bio and press Enter Please contact support clcbio com if you have not received an Order ID Note that if you are upgrading an existing license file this needs to be deleted from the licenses folder When you run the downloadlicense command script it will create a new license file Restart the server for the new license to take effect see how to restart the server in section 2 8 2 2 7 3 Linux license download License files are do
34. ore information If you need assistance please contact Support clcbio com and include the contents of transcript If the initialization is successful the status bar will display this message Database successfully initialized YOU can now close the CLC Bioinformatics Database Tool 2 3 Installing and running the Server Getting the CLC Bioinformatics Database software installed and running involves at minimum these steps 1 Install the software 2 Ensure the necessary port in the firewall is open 3 Download a license 4 Start the Server and or configure it as a service All these steps are covered in this section of the manual Further configuration information including for job nodes grid nodes and External Applications are provided in later chapters CHAPTER 2 INSTALLATION 11 Installing and running the CLC Bioinformatics Database is straightforward However if you do run into troubles please refer to the troubleshooting section in Appendix 6 1 which provides tips on how to troubleshoot problems yourself as well as how to get help 2 3 1 Installing the Server software The installation can only be performed by a user with administrative privileges On some operating systems you can double click on the installer file icon to begin installation Depending on your operating system you may be prompted for your password as shown in figure 2 2 or asked to allow the installation to be performed e On Windows 7 or Vista
35. r hostname or IP address of the CLC Server U lt String gt Valid username for logging on to the CLC Server V Display version W lt String gt Clear text password or domain specific password token In order to trust the certificate the ss1lStore tool must be used sslStore S localhost U root W defaullt P 7778 The server localhost presented an untrusted certificate with the following attributes SUBJECT Common Name localhost Alternative Names N A Organizational Unit Enterprise Organization z CLC BIO Locality Aarhus N State N A Country DK SSUER Common Name localhost Organizational Unit Enterprise Organization CLC Bio Locality Aarhus N State N A Country DK FINGERPRINTS SHA 1 A5 F6 8D C4 F6 F3 CB 44 DO BA 83 E9 36 14 AE 9B 68 9B 9C F9 SHA 256 4B BS OB 04 3C 3A Al E2 D1 BF 87 10 F1 5D EA DD 9B 92 FF E3 C1 C9 9A 35 48 AF F6 98 87 OF 1D A8 Valid From Sep 1 2011 Valid To Aug 31 2012 Trust this certificate yn Once the certificate has been accepted the clcserver program is allowed to connect to the server Bibliography 39 Index Active directory 24 AD 24 Bibliography 39 Command line installation 12 Cores restrict usage 21 CPU restrict usage of 21 Encrypted connection 35 GSSAPI 24 HTTPS 35 Kerberos 24 LDAP 24 Memory allocation 21 permissions 29 Quie
36. s done by setting the option max_allowed_packet 64M InnoDB must be available and configured for the MySQL instance to work properly as the CLC Database You should enable the options in the InnoDB section of your configuration as suggested below Q YOu can set _butfer pool size up to 50 80 5 of RAM but beware of setting memory usage too high innodb_buffer_pool_size 256M innodb_additional_mem_pool_size 20M Set _log_file_size to 25 of buffer pool size innodb_log_file_size 64M innodb_log_buffer_size 8M Innodb flush Llog at trx commit 1 innodb lock wait timeout 50 There appears to be a bug in certain versions of MySQL which can cause the cleanup of the query cache to take a very long time Some time many hours If you experience this you should disable the query log by setting the following option query_cache_size 0 6 3 SSL and encryption The CLC Bioinformatics Database supports SSL communication between the server and its clients e g Workbenches or the CLC Server Command Line Tools This is particularly relevant if the server is accessible over the internet as well as on a local network The default configuration of the server does not use SSL 6 3 1 Enabling SSL on the server A server certificate is required before SSL can be enabled on the CLC Bioinformatics Database This is usually obtained from a Certificate Authority CA like Thawte or Verisign See http en wikipedia org wiki Certifica
37. s using the web interface To create or remove users or change their password Admin Users and groups Manage user accounts This will display the panel shown in figure 4 3 CHAPTER 4 MANAGING USERS AND GROUPS 25 E Users and groups F Manage user accounts Add user account Username Password Verify password I Add User Change password For selected user Set Password Remove selected user Remove User gt Manage groups Figure 4 3 Managing users 4 2 2 Managing groups using the web interface To create or remove groups or change group membership for users Admin 47 Users and groups ZA Manage groups This will display the panel shown in figure 4 4 Users and groups K Manage groups Create new group admin en selected g Remove Group T membership Users Group members gt Figure 4 4 Managing users The same user can be a member of several groups Note that membership of the admin group is used for allowing users access to the admin part of the web interface Users who should have access to the administrative part of the server should CHAPTER 4 MANAGING USERS AND GROUPS 26 be part of the admin group which is the only special group this group is already created for you Note that you will always be able to log in as root with administrative access The functionality of this plug in depends on the user authentication and management system if
38. sport guarantee gt CONFIDENTIAL lt transport guarantee gt lt user data constraint gt lt security constraint gt The above section is commented out in the supplied conf web xml file and just has to be commented in in order for redirection to work Please note that this redirection only works for the browser accessing the web interface When connecting from the Workbench the correct port has CHAPTER 6 APPENDIX 38 to be specified 6 3 4 Logging in using SSL from the CLC Server Command Line Tools The CLC Server Command Line Tools will also automatically detect and use SSL if present on the port it connects to If the certificate is untrusted the clcserver program will refuse to login clceserver S localhost U root W defaullt P 7778 Message Trying to log into server Error SSL Handshake failed Check certificate Option Description A lt Command gt Command to run If not specified the list of commands on the server will be returned C lt Integer gt Specify column width of help output D lt Boolean gt Enable debug mode default false G lt Grid Preset value gt Specify to execute on grid H Display general help I lt Algorithm Command gt Get information about an algorithm 0 lt File gt Output file P lt Integer gt Server port number default 7777 Q0 lt Boolean gt Quiet mode No progress output default false S lt String gt Serve
39. stening on port 80 in order to simplify the URL this can be done in the following way e Navigate to the CLC Server installation directory e Locate the file called server xml in the conf directory e Open the file in a text editor and locate the following section lt Connector port 7777 protocol ATTP 1 1 connectionTimeout 20000 redirect Port e443 gt Change the port value to desired listening port 80 in the example below lt Connector port e0 protocol HITTP 1 1 connectionTimeout 20000 redirectPort 8443 gt Restart the service for the change to take effect see how to restart the server in section 2 8 3 4 Setting the amount of memory available for the JVM When running the CLC Bioinformatics Database the Java Virtual Machine JVM needs to know how much memory it can use This depends on the amount of physical memory RAM and can thus be different from computer to computer Therefore the installer investigates the amount of RAM during installation and sets the amount of memory that the JVM can use On Windows and Linux this value is stored in a property file called ServerType vmoptions e g CLCGenomicsServer vmoptions which contains a text like this KmxoO000m The number 8000 is the amount of memory the CLC Bioinformatics Database is allowed to use This file is located in the installation folder of the the CLC Bioinformatics Database software By default he value is set to 50 of the available RAM
40. t installation 12 RAM 21 Recycle bin 31 References 39 Secure socket layer 35 Silent installation 12 SSL 39 System requirements 6 vmoptions memory allocation 21 Xmx argument 21 40
41. te_authorities A signed certificate in a pkcs12 keystore file is also needed The keystore file is either provided by the CA or it can be generated from the private key used to request the certificate and the signed certificate file from the CA see section 6 3 1 CHAPTER 6 APPENDIX 36 Copy the keystore file to the conf subdirectory of the CLC Bioinformatics Database installation folder Next the server xml file in the conf subdirectory of the CLC Bioinformatics Database installation folder has to be edited to enable SSL connections Add text like the following text to the server xml file lt Connector port 8443 protocol HTTP 1 1 SSLEnabled true maxThreads 150 scheme https secure true clientAuth false sslProtocol TLS keystoreFile conf keystore pkcs12 keystorePass tomcat keystoreType PKCS12 2 Replace keystore pkcs12 with the name of your keystore file and replace tomcat with the password for your keystore The above settings make SSL available on port 8443 The standard non SSL port would still be TTT or whatever you may have configured it to If only SSL connection should be allowed the connector entry for port 7777 can safely be removed from the server xml file Self signed certificates can be generated if only connection encryption is needed See http www akadia com services ssh_test_certificate html for further details Creating a PKCS12 keystore file If the certificate is not supplied in a p
42. the list and click the Delete button CHAPTER 4 MANAGING USERS AND GROUPS Zi S Group management Users Membership Groups All Groups admin everybody LabABCgroup Figure 4 6 Managing groups 4 3 3 Adding users to a group When a new group is created it is empty To assign users to a group click the Membership tab In the Selected group box you can choose among all the groups that have been created When you select a group you will see its members in the list below see figure 4 7 To the left you see a list of all users g Group management Users Membership Groups kel Selected Group admin mi Users Group Members clcuser test_admin test_admin itest_readonly test_user Figure 4 7 Listing members of a group To add or remove users from a group click the Add a or Remove lt 2 buttons To create new users see section 4 3 1 The same user can be a member of Several groups 4 4 User statistics Clicking the User statistics panel will show a summary of the current usage of the server An example is shown in figure 4 8 You can see the number of users currently logged in and you can see the number of sessions for each user The two green dots indicate that this user is logged in twice e g through the Workbench and through the web interface The other two users have been logged in previously CHAPTER 4 MANAGING USERS AND GROUPS 28 dC Configuration dr Queu
43. to start analyses on the server and view the results Find the user manuals and deployment manual for the Workbenches at http www clcbio com usermanuals The following chapter on installation will give you more information about how to obtain and deploy the license for the server Chapter 2 Installation 2 1 Quick installation guide The following describes briefly the steps needed to set up a CLC Bioinformatics Database 3 7 with pointers to more detailed explanation of each step 1 Ol Oo O N O 10 11 2 2 Download and run the server installer As part of the installation choose to start the server section 2 3 Run the license download script that is part of the installation section 2 7 The script will automatically download a license file and place it in the server installation directory under licenses Restart the server section 2 8 Log into the server using a web browser note that the default port is 7777 with username root and password default section 3 Change the root password section 4 1 Configure authentication mechanism and optionally set up users and groups section 4 2 Add data locations section 3 2 Download and install plug ins in the Workbench needed for the Workbench to contact the server section 2 9 Check your server set up using the Check set up link in the upper right corner as described in section 6 1 1 Your server is now ready for use
44. uction The technical set up of a CLC Bioinformatics Database involves both a database back end and a server middle layer that the Workbench connects to This server layer also has a web interface which has very basic capabilities for uploading downloading browsing and searching for data The functionality of the CLC Bioinformatics Database can be extended by installation of Server plug ins The available plug ins can be found at http www clcbio com server_plugins 1 1 System requirements The system requirements of CLC Bioinformatics Database are e Windows XP Windows Vista or Windows 7 Windows Server 2003 or Windows Server 2008 e Mac OS X 10 6 or later However Mac OS X 10 5 8 is supported on 64 bit Intel systems e Linux Red Hat or SUSE e 32 or 64 bit e 256 MB RAM required Minimum 2GB of RAM recommended depending on the type of analysis to be performed 1 2 Licensing There are three kinds of licenses needed for running the CLC Bioinformatics Database e A license for the server This is needed for running the server The license will allow a certain number of sessions i e number of log ins from e g the web interface or the workbench The number of sessions is part of the agreement with CLC bio when you purchase a license e A special license if you are running the server on a grid system this is explained in detail in section CHAPTER 1 INTRODUCTION T e A license for the workbench The Workbench is needed
45. wnloaded using the downloadlicense script Run the script and paste the Order ID supplied by CLC bio Please contact support clcbio com if you have not received an Order ID Note that if you are upgrading an existing license file this needs to be deleted from the licenses folder When you run the downloadlicense script it will create a new license file Restart the server for the new license to take effect Restarting the server is covered in in CHAPTER 2 INSTALLATION AALA Terminal bash 79x24 mazcbook 1 17 aandersen HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH H CLO bio License download utility HH HHHHHHHHHHHHHHHHHHHHHHHRHHHHHHHHRHHRHRHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Hostname host Host IDGS15 Xxx Please enter for copy paste your License Order ID and press return Figure 2 6 Download a license based on the Order ID section 2 8 3 2 8 Starting and stopping the server 2 8 1 Microsoft Windows 15 On Windows based systems the CLC Bioinformatics Database can be controlled through the Services control panel Choose the service called CLCBioinformaticsDatabase and click the start stop or restart link as shown in figure 2 7 Services File Action View Help 1 B R Ry Services Local un L ocal CLCServer Name Description S Sa Background Intelligent Transfer Service Transfers files in the background a he ae a Sne Bal ala CLC Genomics Server iae S Sa

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