[apollo] New Apollo Release 2.0.5(JB#9334e76fd)

[Monica Munoz-Torres]

*We are pleased to announce the latest Apollo release*

*Apollo 2.0.5 *

*Some of the new features include:*

- Numerous UI and performance improvements, including easier navigation
between annotated elements via the Annotator Panel.
- Better server and client-side reporting.
- It is now possible to also include metadata on import.
- Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
- Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 (
#9334e76fd
<https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>).
Use ./apollo clean-all or install from a formal release download for best
performance.


*Some important bug fixes:*

- Import script were logging preferences unnecessarily.
- Improved security for non-public genomes.
- Fixed for going between logged-out mode and the Annotator Panel while
retaining history.
- Improved display of sequence over the annotation after moving the
annotation to the opposite strand.
- Users will see a warning message when it is not possible to create an
intron with canonical splice sites in the selected region.


* The *latest release* can be downloaded from GitHub at:
https://github.com/GMOD/Apollo/releases/latest

* *Detailed, searchable documentation* on pre-requisites, configuration,
and installation guides found at:
http://genomearchitect.readthedocs.io/

* A more *detailed account of all changes* is available in the Apollo
ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo
instances running, you can use your current JBrowse data directories. The
quick-start guide is available at: http://genomearchitect.rea
dthedocs.io/en/stable/Apollo2Build.html

* *Migrating existing annotations:* Please find detailed information about
migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html

** Troubleshooting, GitHub tracker, Mailing List: *

- Browse the Troubleshooting guide at http://genomearchitect.readthe
docs.io/en/stable/Troubleshooting.html
<http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
- Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
- Post your questions on our mailing list at ***@lists.lbl.gov

* *The Apollo User Guide* is available at http://genomearchitect.org/use
rs-guide/

** Public Demo: If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo
Demo at http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>*

* These and more details are available at the Apollo Website
<http://genomearchitect.org/> and the Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.


We look forward to your questions and suggestions.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>

[image: Inline image 1]

It is very likely you will receive this message more than once; we offer
our sincere apologies for the redundancy.
Bee photograph by www.AlexanderWild.com
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

[Nathan Dunn]

We have updated our Docker release (thanks Eric Rasche) for 2.0.5 + Chado: https://github.com/GMOD/docker-apollo/releases <https://github.com/GMOD/docker-apollo/releases>

We have released AMI images updated for 2.0.5 (Java 8, Tomcat 8, Ubuntu 16.04) on Amazon Web Services (AWS) in most regions. They should be available shortly.

Please let us know if you experience any issues via a GitHub issue or this list.

Thank you,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory

Post by Monica Munoz-Torres
We are pleased to announce the latest Apollo release
Apollo 2.0.5
Numerous UI and performance improvements, including easier navigation between annotated elements via the Annotator Panel.
Better server and client-side reporting.
It is now possible to also include metadata on import.
Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 (#9334e76fd <https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>). Use ./apollo clean-all or install from a formal release download for best performance.
Import script were logging preferences unnecessarily.
Improved security for non-public genomes.
Fixed for going between logged-out mode and the Annotator Panel while retaining history.
Improved display of sequence over the annotation after moving the annotation to the opposite strand.
Users will see a warning message when it is not possible to create an intron with canonical splice sites in the selected region.
https://github.com/GMOD/Apollo/releases/latest <https://github.com/GMOD/Apollo/releases/latest>
http://genomearchitect.readthedocs.io/ <http://genomearchitect.readthedocs.io/>
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html <http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html>
* Migrating existing annotations: Please find detailed information about migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html <http://genomearchitect.readthedocs.io/en/latest/Migration.html>
Browse the Troubleshooting guide at http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html <http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
Open a GitHub issue at https://github.com/GMOD/Apollo/issues/ <https://github.com/GMOD/Apollo/issues/>
* The Apollo User Guide is available at http://genomearchitect.org/users-guide/ <http://genomearchitect.org/users-guide/>
* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>
* These and more details are available at the Apollo Website <http://genomearchitect.org/> and the Apollo repository <https://github.com/GMOD/Apollo/blob/master/README.md>.
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>
<Hackathon-logo-image.png>
It is very likely you will receive this message more than once; we offer our sincere apologies for the redundancy.
Bee photograph by www.AlexanderWild.com <http://www.alexanderwild.com/>
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

[Loraine Guéguen]

Great job!

"It is now possible to also include metadata on import"
I am not sure (and cannot find in the demo suited data to test that
point): does this mean that with release 2.0.5 all the metadata included
in a feature in an evidence track (Go terms, Ec numbers, notes...) can
be kept when creating an annotation from this feature ?

"Upgrade to Java 8 / GWT 2.8"
Release 2.0.5 is not compatible with Java 7 anymore, is it ?

Thanks

Loraine Guéguen

Post by Monica Munoz-Torres
*We are pleased to announce the latest Apollo release*
*Apollo 2.0.5
*
*Some of the new features include:*
* Numerous UI and performance improvements, including easier
navigation between annotated elements via the Annotator Panel.
* Better server and client-side reporting.
* It is now possible to also include metadata on import.
* Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
* Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09
(#9334e76fd
<https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>).
Use ./apollo clean-all or install from a formal release download
for best performance.
*
*Some important bug fixes:*
*
* Import script were logging preferences unnecessarily.
* Improved security for non-public genomes.
* Fixed for going between logged-out mode and the Annotator Panel
while retaining history.
* Improved display of sequence over the annotation after moving the
annotation to the opposite strand.
* Users will see a warning message when it is not possible to create
an intron with canonical splice sites in the selected region.
https://github.com/GMOD/Apollo/releases/latest
<https://github.com/GMOD/Apollo/releases/latest>
* *Detailed, searchable documentation* on pre-requisites,
http://genomearchitect.readthedocs.io/
<http://genomearchitect.readthedocs.io/>
* A more *detailed account of all changes* is available in the Apollo
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md
<https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
* *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo
instances running, you can use your current JBrowse data directories.
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html
<http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html>
* *Migrating existing annotations:* Please find detailed information
about migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html
<http://genomearchitect.readthedocs.io/en/latest/Migration.html>
*
** Troubleshooting, GitHub tracker, Mailing List: *
*
* Browse the Troubleshooting guide at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
<http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
* Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
<https://github.com/GMOD/Apollo/issues/>
* *The Apollo User Guide* is available at
http://genomearchitect.org/users-guide/
<http://genomearchitect.org/users-guide/>
*
** Public Demo:*If you are new to Apollo we encourage you to learn
more about our software and its functionality by taking a tour of our
Apollo Demo at http://genomearchitect.org/demo/
<http://genomearchitect.org/demo/>
*
* These and more details are available at the Apollo Website
<http://genomearchitect.org/> and the Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>
Inline image 1
It is very likely you will receive this message more than once; we
offer our sincere apologies for the redundancy.
Bee photograph by www.AlexanderWild.com <http://www.AlexanderWild.com>
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

[Nathan Dunn]

Post by Loraine Guéguen
Great job!
"It is now possible to also include metadata on import"
I am not sure (and cannot find in the demo suited data to test that point): does this mean that with release 2.0.5 all the metadata included in a feature in an evidence track (Go terms, Ec numbers, notes...) can be kept when creating an annotation from this feature ?

The fix is that when you are importing via this script:

https://github.com/GMOD/Apollo/blob/master/tools/data/add_transcripts_from_gff3_to_annotations.pl <https://github.com/GMOD/Apollo/blob/master/tools/data/add_transcripts_from_gff3_to_annotations.pl>

via your reported bug:

https://github.com/GMOD/Apollo/issues/1146#issuecomment-235767302 <https://github.com/GMOD/Apollo/issues/1146#issuecomment-235767302>

There is a “-X” option as well that disables the CDS recalculation by Apollo, but possibly someone else had asked for that.

Post by Loraine Guéguen
"Upgrade to Java 8 / GWT 2.8"
Release 2.0.5 is not compatible with Java 7 anymore, is it ?

That is correct. In general Java 7 is not officially supported, either. If you absolutely needed a way to work around it you could, but I think that just upgrading to Java 8 would be the bet.


Nathan

Post by Loraine Guéguen
Thanks
Loraine Guéguen

Post by Monica Munoz-Torres
We are pleased to announce the latest Apollo release
Apollo 2.0.5
Numerous UI and performance improvements, including easier navigation between annotated elements via the Annotator Panel.
Better server and client-side reporting.
It is now possible to also include metadata on import.
Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 (#9334e76fd <https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>). Use ./apollo clean-all or install from a formal release download for best performance.
Import script were logging preferences unnecessarily.
Improved security for non-public genomes.
Fixed for going between logged-out mode and the Annotator Panel while retaining history.
Improved display of sequence over the annotation after moving the annotation to the opposite strand.
Users will see a warning message when it is not possible to create an intron with canonical splice sites in the selected region.
https://github.com/GMOD/Apollo/releases/latest <https://github.com/GMOD/Apollo/releases/latest>
http://genomearchitect.readthedocs.io/ <http://genomearchitect.readthedocs.io/>
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html <http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html>
* Migrating existing annotations: Please find detailed information about migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html <http://genomearchitect.readthedocs.io/en/latest/Migration.html>
Browse the Troubleshooting guide at http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html <http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
Open a GitHub issue at <https://github.com/GMOD/Apollo/issues/>https://github.com/GMOD/Apollo <https://github.com/GMOD/Apollo>/issues/
* The Apollo User Guide is available at http://genomearchitect.org/users-guide/ <http://genomearchitect.org/users-guide/>
* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at <http://genomearchitect.org/demo/>http://genomearchitect.org/dem <http://genomearchitect.org/dem>o/
* These and more details are available at the Apollo Website <http://genomearchitect.org/> and the Apollo repository <https://github.com/GMOD/Apollo/blob/master/README.md>.
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>
<Mail Attachment.png>
It is very likely you will receive this message more than once; we offer our sincere apologies for the redundancy.
Bee photograph by <http://www.alexanderwild.com/>www.AlexanderWild.com <http://www.alexanderwild.com/>
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Nathan Dunn]

Loraine,

To clarify when you export a GFF3 in Apollo, if you import the same GFF3 using the add_transcripts_from_gff3_to_annotations.pl all of the metadata will be preserved.

If the metadata of your evidence is in the Apollo GFF3 format for column 9, it will be imported this way.

When you drag up evidence into the manual annotation region, we do not pull in metadata by design as it is considered a synthesis of the underlying metadata and should be merged with any underlying GFF3 during export.

Nathan

Post by Nathan Dunn

Post by Loraine Guéguen
Great job!
"It is now possible to also include metadata on import"
I am not sure (and cannot find in the demo suited data to test that point): does this mean that with release 2.0.5 all the metadata included in a feature in an evidence track (Go terms, Ec numbers, notes...) can be kept when creating an annotation from this feature ?

https://github.com/GMOD/Apollo/blob/master/tools/data/add_transcripts_from_gff3_to_annotations.pl <https://github.com/GMOD/Apollo/blob/master/tools/data/add_transcripts_from_gff3_to_annotations.pl>
https://github.com/GMOD/Apollo/issues/1146#issuecomment-235767302 <https://github.com/GMOD/Apollo/issues/1146#issuecomment-235767302>
There is a “-X” option as well that disables the CDS recalculation by Apollo, but possibly someone else had asked for that.

Post by Loraine Guéguen
"Upgrade to Java 8 / GWT 2.8"
Release 2.0.5 is not compatible with Java 7 anymore, is it ?

That is correct. In general Java 7 is not officially supported, either. If you absolutely needed a way to work around it you could, but I think that just upgrading to Java 8 would be the bet.
Nathan

Post by Loraine Guéguen
Thanks
Loraine Guéguen

Post by Monica Munoz-Torres
We are pleased to announce the latest Apollo release
Apollo 2.0.5
Numerous UI and performance improvements, including easier navigation between annotated elements via the Annotator Panel.
Better server and client-side reporting.
It is now possible to also include metadata on import.
Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 (#9334e76fd <https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>). Use ./apollo clean-all or install from a formal release download for best performance.
Import script were logging preferences unnecessarily.
Improved security for non-public genomes.
Fixed for going between logged-out mode and the Annotator Panel while retaining history.
Improved display of sequence over the annotation after moving the annotation to the opposite strand.
Users will see a warning message when it is not possible to create an intron with canonical splice sites in the selected region.
https://github.com/GMOD/Apollo/releases/latest <https://github.com/GMOD/Apollo/releases/latest>
http://genomearchitect.readthedocs.io/ <http://genomearchitect.readthedocs.io/>
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html <http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html>
* Migrating existing annotations: Please find detailed information about migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html <http://genomearchitect.readthedocs.io/en/latest/Migration.html>
Browse the Troubleshooting guide at http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html <http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
Open a GitHub issue at <https://github.com/GMOD/Apollo/issues/>https://github.com/GMOD/Apollo <https://github.com/GMOD/Apollo>/issues/
* The Apollo User Guide is available at http://genomearchitect.org/users-guide/ <http://genomearchitect.org/users-guide/>
* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at <http://genomearchitect.org/demo/>http://genomearchitect.org/dem <http://genomearchitect.org/dem>o/
* These and more details are available at the Apollo Website <http://genomearchitect.org/> and the Apollo repository <https://github.com/GMOD/Apollo/blob/master/README.md>.
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>
<Mail Attachment.png>
It is very likely you will receive this message more than once; we offer our sincere apologies for the redundancy.
Bee photograph by <http://www.alexanderwild.com/>www.AlexanderWild.com <http://www.alexanderwild.com/>
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

[Loraine Guéguen]

Hi,

Is Apollo release 2.0.4 compatible with Java 8 ?

Loraine Guéguen

Post by Nathan Dunn

On Jan 5, 2017, at 5:22 AM, Loraine Guéguen
Great job!
"It is now possible to also include metadata on import"
I am not sure (and cannot find in the demo suited data to test that
point): does this mean that with release 2.0.5 all the metadata
included in a feature in an evidence track (Go terms, Ec numbers,
notes...) can be kept when creating an annotation from this feature ?

https://github.com/GMOD/Apollo/blob/master/tools/data/add_transcripts_from_gff3_to_annotations.pl
https://github.com/GMOD/Apollo/issues/1146#issuecomment-235767302
There is a “-X” option as well that disables the CDS recalculation by
Apollo, but possibly someone else had asked for that.

"Upgrade to Java 8 / GWT 2.8"
Release 2.0.5 is not compatible with Java 7 anymore, is it ?

That is correct. In general Java 7 is not officially supported,
either. If you absolutely needed a way to work around it you could,
but I think that just upgrading to Java 8 would be the bet.
Nathan

Thanks
Loraine Guéguen

Post by Monica Munoz-Torres
*We are pleased to announce the latest Apollo release*
*Apollo 2.0.5
*
*Some of the new features include:*
* Numerous UI and performance improvements, including easier
navigation between annotated elements via the Annotator Panel.
* Better server and client-side reporting.
* It is now possible to also include metadata on import.
* Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
* Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09
(#9334e76fd
<https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>).
Use ./apollo clean-all or install from a formal release download
for best performance.
*
*Some important bug fixes:*
*
* Import script were logging preferences unnecessarily.
* Improved security for non-public genomes.
* Fixed for going between logged-out mode and the Annotator Panel
while retaining history.
* Improved display of sequence over the annotation after moving
the annotation to the opposite strand.
* Users will see a warning message when it is not possible to
create an intron with canonical splice sites in the selected region.
https://github.com/GMOD/Apollo/releases/latest
<https://github.com/GMOD/Apollo/releases/latest>
* *Detailed, searchable documentation* on pre-requisites,
http://genomearchitect.readthedocs.io/
<http://genomearchitect.readthedocs.io/>
* A more *detailed account of all changes* is available in the
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md
<https://github.com/GMOD/Apollo/blob/master/ChangeLog.md>
* *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo
instances running, you can use your current JBrowse data
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html
<http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html>
* *Migrating existing annotations:* Please find detailed information
about migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html
<http://genomearchitect.readthedocs.io/en/latest/Migration.html>
*
** Troubleshooting, GitHub tracker, Mailing List: *
*
* Browse the Troubleshooting guide at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
<http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
* Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
* *The Apollo User Guide* is available at
http://genomearchitect.org/users-guide/
<http://genomearchitect.org/users-guide/>
*
** Public Demo:*If you are new to Apollo we encourage you to learn
more about our software and its functionality by taking a tour of
our Apollo Demo at http://genomearchitect.org/demo/
*
* These and more details are available at the Apollo Website
<http://genomearchitect.org/> and the Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>
<Mail Attachment.png>
It is very likely you will receive this message more than once; we
offer our sincere apologies for the redundancy.
Bee photograph by www.AlexanderWild.com
--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720
This list is for the Apollo Annotation Editing Tool. Info athttp://genomearchitect.org/

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Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
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http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

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Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

[Lbl]

Yes.

Nathan

Post by Loraine Guéguen
Hi,
Is Apollo release 2.0.4 compatible with Java 8 ?
Loraine Guéguen

Post by Nathan Dunn

Post by Loraine Guéguen
Great job!
"It is now possible to also include metadata on import"
I am not sure (and cannot find in the demo suited data to test that point): does this mean that with release 2.0.5 all the metadata included in a feature in an evidence track (Go terms, Ec numbers, notes...) can be kept when creating an annotation from this feature ?

https://github.com/GMOD/Apollo/blob/master/tools/data/add_transcripts_from_gff3_to_annotations.pl
https://github.com/GMOD/Apollo/issues/1146#issuecomment-235767302
There is a “-X” option as well that disables the CDS recalculation by Apollo, but possibly someone else had asked for that.

Post by Loraine Guéguen
"Upgrade to Java 8 / GWT 2.8"
Release 2.0.5 is not compatible with Java 7 anymore, is it ?

That is correct. In general Java 7 is not officially supported, either. If you absolutely needed a way to work around it you could, but I think that just upgrading to Java 8 would be the bet.
Nathan

Post by Loraine Guéguen
Thanks
Loraine Guéguen

Post by Monica Munoz-Torres
We are pleased to announce the latest Apollo release
Apollo 2.0.5
Numerous UI and performance improvements, including easier navigation between annotated elements via the Annotator Panel.
Better server and client-side reporting.
It is now possible to also include metadata on import.
Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 (#9334e76fd). Use ./apollo clean-all or install from a formal release download for best performance.
Import script were logging preferences unnecessarily.
Improved security for non-public genomes.
Fixed for going between logged-out mode and the Annotator Panel while retaining history.
Improved display of sequence over the annotation after moving the annotation to the opposite strand.
Users will see a warning message when it is not possible to create an intron with canonical splice sites in the selected region.
https://github.com/GMOD/Apollo/releases/latest
http://genomearchitect.readthedocs.io/
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md
* Quick-Start Guide for Apollo 2.0.x: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html
* Migrating existing annotations: Please find detailed information about migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html
Browse the Troubleshooting guide at http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
* The Apollo User Guide is available at http://genomearchitect.org/users-guide/
* Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/
* These and more details are available at the Apollo Website and the Apollo repository.
We look forward to your questions and suggestions.
Sincerely,
The Apollo Development Team
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It is very likely you will receive this message more than once; we offer our sincere apologies for the redundancy.
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Mentorship Matters!
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Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/