FAQs

1.  Check your catalina.log file to make sure that there are not any errors on startup.

2. What build target did you use?  If you use all-tomcat, then the GNomExLDAPRealm should be in use, but if you build with all-tomcat-opensource, then the GNomExRealm is activated and that realm only authenticates using the external user name and password stored in the GNomEx db.

3.  [Univ of Utah ONLY] Make sure that the carcerts file that allows access to the UofU LDAP servers is in the java that Tomcat runs under.  (You should be running with JDK 1.7, not 1.8 since we haven’t validated against this version yet.)  If you installed Tomcat for Windows, it seems like you should be able to see the path to the java executable.

OR

4.  Look at your catalina.properties to make sure that the LDAP properties are not commented out.  (Unlikely…)  If you have recently modified your catalina.properties, try deleting the Tomcat local cache and restarting to make sure it is picking up your most recent changes.  The local cache is in /path/to/tomcat/conf/Catalina/localhost.

5.  What gnomex DB are you pointing to in your catalina.properties?

6.  Put a breakpoint in GNomExLDAPRealm is authenticate() use Tomcat Remote Debugging to step into the code.  Does the GNomEx db connection work?  Does the select from AppUser return a row and isActive = ‘Y’ on the AppUser?

You may need to deleted the directory /path/to/apache-tomcat/webapps/gnomex.  Then the gnomex.war will expand with brand new contents.  The other possibility is Apache Tomcat has cached something.  Try deleted the following directories and restarting Apache Tomcat:

/path/to/apache-tomcat/conf/Catalina

/path/to/apache-tomcat/work/Catalina

/path/to/apache-tomcat/temp

The jnlps are downloaded into an obscure tmp directory and never launched.  So one must find them and manually double click. No way around this.  To get them to go to your Downloads folder, deselect the "Open 'safe' files after downloading" toggle under Safari's Preferences -> General.

Please make sure that gnomex_ldap_connection.properties file is placed in the /properties directory. Then specify your LDAP connection properties here.

Depending on your LDAP, you may need to disable SSL support. In this case, comment out the uofu_ldap_sec_protocol=ssl and change the uofu_ldap_provider_url from ldaps://server:sslPort toldap://server:389.

# ldap properties  uofu_ldap_init_context_factory=com.sun.jndi.ldap.LdapCtxFactory  uofu_ldap_provider_url=ldap://servername.somewhere.someplace.edu:636/dc=someplace,dc=edu  uofu_ldap_sec_protocol=ssl  uofu_ldap_sec_auth=simple    # db properties  dbUsername=gnomex  dbPassword=gnomex_db_password_goes_here  dbDriver=com.mysql.jdbc.Driver  dbURL=jdbc:mysql://localhost:3306/gnomex

GNomEx should work properly under Chrome. Check the version of the flash player plugin to make sure it is up-to-date. From the main URL (address) field, type chrome://plugins. Then look for Adobe Flash Player and find out what version you are running.

If you are running an old version of the Flash Player Plug-in, please visit the Adobe Flash Player download page to get the latest player.

You can create multiple core facilities in GNomEx. Go to Add/Edit Dictionaries (Menu item Config -> Add/Edit Dictionaries). Click on the "General – Core Facilities" folder. GNomEx ships with a default core facility. You can add other core facilities here. You can name these whatever you want.  Then in "Configure Experiment Platforms", you will associate an experiment platform with a core facility.

The installation comes with a default super admin account (user = admin, password = admin). Login with this account and then you can create other super admin accounts. When you have a super admin account created, delete the default "admin" user.

Yes. There is a java class hci.gnomex.security.SecurityManager which connects to an LDAP server. The LDAP connect properties are passed in to the class from the /properties/gnomex_ldap_connection.properties. Here is an example properties file:

# ldap properties
uofu_ldap_init_context_factory=com.sun.jndi.ldap.LdapCtxFactory
uofu_ldap_provider_url=ldap://servername.somewhere.someplace.edu:636/dc=someplace,dc=edu
uofu_ldap_sec_protocol=ssl
uofu_ldap_sec_auth=simple

# db properties dbUsername=gnomex
dbPassword=gnomex_db_password_goes_here
dbDriver=com.mysql.jdbc.Driver
dbURL=jdbc:mysql://localhost:3306/gnomex

External experiments provide a mechanism for uploading the data files. GNomex distinguished external experiments (user is registering experiment results in the GNomEx repository) from submitted experiment requests (user is requesting an experiment to be performed by the core facility). In the latter case, the core facility will be placing the files directly on the file server. (See FAQ for details on the experiment file directory structure on the file server).

The Analysis feature provides a repository for analysis performed on the raw experiment files. The analyzed data files are cataloged here along with annotations that categorize and describe the data analysis performed. Analysis entries can be versioned (through Analysis Groups) and linked to the original experiment.

Q:  When I click "Billing", then select period, group, and account, and found that "Experiment" is still "Pending"…. When I click "Invoice", I got "Please complete the billing items first." After I checked the "Workflow", I finished all the steps from "Sample Quality" to "QA Pipeline", and I can find some items from "Flow Cells". Could you please let me know if I forget the last step or any other step to change the status of a project from "pending" to "completed" when I click "Billing" and "Experiment"?

A: GNomEx creates "Pending" billing items for each experiment, which are estimated charges for the experiment and may not take into account exceptions that occur during experiment processing. Even though an experiment has been completed through the workflow, it requires manual review of the billing items in order to ensure accuracy and completeness. The billing screens were designed to be used for a once-a-month billing cycle. (Billing cycles can be configured for a different time span.)

At this time, the our core facility needs manual control over the invoicing since some experiments span multiple billing periods or have charges split between multiple billing accounts from different labs; therefore GNomEx has not yet automated changing the billing status from "Pending" to "Completed". In addition, our core facility found it useful to have a further level of review/control over invoicing — billing item status must be changed to "Approved" before the final invoice is sent out (auto-emailed to the lab"s billing contact).

You need to run the batch job to build the Lucene index files. Instructions for running this script are provided in the README_INSTALL.txt in the GNomEx download. At our facility, we run this batch job nightly, so searches will not include experiments submitted during the day. It is possible to run this script on a more frequent basis.

(3) Pick the account to be billed." -- "If billing account is inactive, please download the work authorization form below. Forward the completed form to the ENTER FACILITY NAME HERE (ENTER ROOM AND PHONE NUMBER HERE)."

These are properties that can be configured through Dictionaries. You can edit the properties using the 'Configure…' link in the GNomEx nav bar and select the 'Add/Edit Dictionaries' menu item. From the Dictionary Editor, click on the folder title 'Admin – Properties'. The properties to edit are 'contact_name_core_facility' and 'contact_email_core_facility' Many other notes, instructions, and links are configurable through these properties.

Many of the GNomEx features are described in a paper published in BMC Bionformatic. Also, Look in the GNomEx download folder gnomex/docs which contains a FAQ, a configuration guide (first draft), and a class diagram.

Set the environment variable before running the ant build:

set ANT_OPTS=-Xms512m -Xmx512m (Windows) export ANT_OPTS=”-Xms512m -Xmx512m” (ksh/bash) setenv ANT_OPTS “-Xms512m -Xmx512m” (tcsh/csh)

You will need to set the <mail-session> properties in /path/to/orion/config.xml. Here is an example of how to set the properties:

<mail-session location="mail/MailSession" smtp-host="smtp.gmail.com">
<property name="mail.smtp.starttls.enable" value="true" />
<property name="mail.transport.protocol" value="smtp" />
<property name="mail.smtp.port" value="465" />
<property name="mail.smtp.auth" value="true" />
<property name="mail.smtp.user" value="first.last@gmail.com" />
<property name="mail.smtp.password" value="gmail_password_goes_here" />
<property name="mail.smtp.debug" value="true" />
<property name="mail.smtp.socketFactory.class" value="javax.net.ssl.SSLSocketFactory"/>
<property name="mail.smtp.socketFactory.port" value="465"/>
<property name="mail.smtp.socketFactory.fallback" value="false"/> </mail-session>

If you plan on making significant changes to the user interface, I would suggest purchasing Flash Builder 4, which costs ~ $250. This is an Eclipse based development environment for building Flex applications. It will allow you to design the Flex screens in an interactive drag-and-drop environment.

GNomEx currently compiles using the Flex SDK 3.5, which is packaged into Flash Builder 4. In the coming months, I will most likely port GNomEx to the Flex SDK 4.

If you are making very small changes to the software, you might be able to manage with a good text editor, the Java SDK, the open source Flex SDK, and Ant. (See README_INSTALL.txt for notes on how to build GNomEx.) Another option is to use Eclipse (http://www.eclipse.org/) as your development environment, which offers a robust Java IDE for modifying, building, and debugging the code, only without the ability to design and debug the Flex application interactively.

To be able to download data files from GNomEx, you will need to set the following properties to point GNomEx to a file directory on your server (or mounted on your server) that is read accessible to the account your are running the Orion application server under. experiment_directory – The path to the root experiment directory. GNomEx assumes that this directory contains subdirectories for each year; the year subdirectory contains subdirectories for each request number. Here is an example:

       /home/gnomex/experiments
2009
2010
6445R Your next-gen sequencing read files go here or in subdirectories here. You will need to copy/move your data files here to make them available for download. 6446R flowcell_directory - The path to the root flowcell quality report directory. GNomEx assumes that this directory contains subdirectories for each year; the year subdirectoriy contains subdirectories for each flow cell number: Here's an example /home/gnomex/flowcellqc 2009 2010 FC10 You flowcell quality report goes here

You can set the flowcell_directory and experiment_directory in GNomEx by clicking on the dictionaries link (right corner of nav bar). Click on the folder called ‘Admin Properties’, then set each property. (Remember to press the ‘Save’ button.)

When you select the experiment, then click the ‘Download’ link at the bottom, you should see the experiment downloads folder. Check the folder and then click on ‘˜Explore files’. This will display all of the files sitting in the experiment directory ready for download.