IGB 10.0.0 released

[Nowlan Freese]

We are excited to announce that we have released IGB 10.0.0

Some highlights:

• Fixed an issue where the IGB installer would disappear during installation.
• Fixed an issue where IGB would crash unexpectedly.
• Added support for CRAM files.
• Added support for nucleotide symbols when searching for residues in the Advanced Search tab.
• Exons are now numbered ("block number") when using the tooltips or Selection Info tab.
• Updated list of restriction enzymes.

Please let us know if you experience any issues!

Full release notes
New Feature
IGBF-3236 - Interpret nucleotide symbols when searching by residue
IGBF-2976 - Add exon number to selection info
IGBF-3478 - Add CRAM support to IGB

Improvement

IGBF-3370 - Add link to advanced search info to IGB interface
IGBF-3484 - Update htsjdk-igb to 3.0.0

IGBF-3465 - Update BigWig/BigBed htsjdk-igb version

IGBF-3335 - Update IGB java 1.8 dependencies

IGBF-3431 - Update maven-bundle-plugin

IGBF-3548 - Updating Restriction Enzyme's in IGB

Task

IGBF-3566 - Clean up IGB project/main/shared-lib-wrapper poms
IGBF-3508 - Create Install4J v10 Docker image for JDK21

IGBF-3464 - Deploy htsjdk-igb

IGBF-3451 - Clean up R6 commits, create pull request to main-JDK8

IGBF-3430 - Remove osgi compendium from the IGB Project

IGBF-3379 - Edit SCR annotations to use R6 instead of R5 syntax and observe the effects

IGBF-3382 - Remove remote error dependencies

IGBF-3637 - Investigate: How to sign Linux installers

IGBF-1469 - Investigate supporting CRAM files

Bug

IGBF-3311 - Investigate org.slf4j.api error

IGBF-3310 - Investigate com.google.guava error

IGBF-3304 - Fix the shared-lib-wrapper maven-dependency-plugin version

IGBF-3350 - Fix guava error when running IGB from Netbeans

IGBF-3521 - Investigate build problem: effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0

IGBF-3414 - Investigate: Update Core/IGB error

IGBF-3522 - Investigate build problem: unknown parameter ignoreChecksumFailure

IGBF-3422 - Investigate Test Failure that is occurring in QuickloadUtilsTest class.

IGBF-3412 - Investigate: Update Core/DAS error

IGBF-3441 - Fix DAS error

IGBF-3525 - Investigate build problem: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder"

IGBF-3564 - Fix remove duplicate package warning

IGBF-3561 - Fix source value 8 is obsolete in JDK21

IGBF-3560 - Fix unknown enum constant XmlAccessType.FIELD

IGBF-3567 - Fix service component warning

IGBF-3563 - Fix warning java.lang.Float has been deprecated

IGBF-3597 - Investigate error that occurs when loading URLs via a script on Windows

Documentation

IGBF-3386 - Update IGB project documentation to explain new main development branch naming scheme

[加藤紗智]

I have updated to ver.10.0.0. But it could not apply .useq file and it shows "FORMAT NOT RECOGNIZED".

I also tried to upload .useq file which could upload previously, but same error message displayed.

I checked "Species" and "Genome version". What was wrong? Is there any suggestions?

Thanks,

Sachi

2024年3月7日木曜日 5:18:25 UTC+9 Nowlan Freese:

[Nowlan Freese]

Hi Sachi,

USEQ support was removed in 2022 for IGB 9.1.10. I will look to see if we can add USEQ support back to IGB for the next release. In the meantime, I would suggest downloading IGB 9.1.8 from SourceForge and install it on your computer as it should be the most recent version of IGB to support USEQ: https://sourceforge.net/projects/genoviz/files/IGB%209.1.8/

Sorry for the trouble!

Nowlan

[加藤紗智]

Hi Nowlan,

Thank you for your advice and let me know about IGB version.  I will try it!

Sachi

2024年4月24日水曜日 22:23:29 UTC+9 Nowlan Freese:

[Nowlan Freese]

Hi Sachi,

We were able to add back support for USEQ in IGB. You can download the IGB Early Access version with USEQ support here: https://www.bioviz.org/earlyAccessDownload.html

We don't have a lot of USEQ files to test, so if you are able to try it out and let us know how it works that would be great!

Thank you!

Nowlan