Details
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Type: Documentation
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Status: Closed (View Workflow)
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Priority: Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Epic Link:
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Sprint:Summer 2: 22 Jun - 3 Jul
Description
Earlier in the month we received a notification from a user that IGB was failing to build on a Debian system.
Turns out the problem was lack of JavaFX on the system.
To make sure others do not encounter the same problem, we should check into this a bit more. Let's clarify which versions of Java can be installed using Debian package managers versus having to download them from Oracle. Let's summarize what we find here (in this ticket) and then update the README.md on the IGB repository.
See:
https://groups.google.com/forum/#!topic/integrated-genome-browser-help-desk/B5ReR-c_Po8
Attachments
Issue Links
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IGBF-2459 Post to Developers Group explaining how to build on Debian
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Activity
Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
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Epic Link | IGBF-1531 [ 17617 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Assignee | Chester Dias [ cdias1 ] |
Ann Loraine
made changes -
Assignee | Chester Dias [ cdias1 ] | Chaitanya Kintali [ chaitanya ] |
Ann Loraine
made changes -
Assignee | Chaitanya Kintali [ chaitanya ] |
Chester Dias (Inactive)
made changes -
Assignee | Chester Dias [ cdias1 ] |
Chester Dias (Inactive)
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Chester Dias (Inactive)
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Attachment | Build logs [ 14770 ] |
Chester Dias (Inactive)
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Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Chester Dias (Inactive)
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Assignee | Chester Dias [ cdias1 ] | Ann Loraine [ aloraine ] |
Ann Loraine
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Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
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Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
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Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
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Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
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Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
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Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Ann Loraine
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Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] | Chester Dias [ cdias1 ] |
Ann Loraine
made changes -
Cause of error and failure in build occurred due to below issue
igb-javafx-util: Compilation failure
This package needs java fx to be present
Testing is done on Debian 9(Stretch) using Maven: 3.6.3
Installation of oracle java was not successful on this OS with the default packages link showing 404 error in the apt installer.
Alternatively, I used the openjdk8 installation
This package does not have javafx by default and has to be installed seperately using below command
This builds the application successfully. Attached is the build details from the Debian 9 OS
Debian 10 does not seem to have openjdk available in its default repositories.
Below are the steps to install oracle java jdk on Debian 10.Note to the user: Ensure the right architecture package is used (either X64 java for 64 bit OS and X86 for a 32 bit OS)
Step 1. Download the correct Java from https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html
This built IGB successfully on Debian 10(Buster)
[~aloraine] Please let me know if I should update the README.md to include the steps