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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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* A more detailed account of all changes is available in the Apollo ChangeLog: 

* 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 

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

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




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: [apollo-dev] New Apollo Release 2.0.5(JB#9334e76fd)

nathandunn

We have updated our Docker release (thanks Eric Rasche) for 2.0.5 + Chado: 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
[hidden email]


On Dec 9, 2016, at 10:39 AM, Monica Munoz-Torres <[hidden email]> wrote:

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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* A more detailed account of all changes is available in the Apollo ChangeLog: 

* 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 

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

<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



-- 
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





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New Apollo Release 2.0.5(JB#9334e76fd)

Loraine Guéguen
In reply to this post by Monica Munoz-Torres
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


Le 09/12/2016 19:39, Monica Munoz-Torres a écrit :
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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* A more detailed account of all changes is available in the Apollo ChangeLog: 

* 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 

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

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




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New Apollo Release 2.0.5(JB#9334e76fd)

nathandunn

On Jan 5, 2017, at 5:22 AM, Loraine Guéguen <[hidden email]> wrote:

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:


via your reported bug:


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


Le 09/12/2016 19:39, Monica Munoz-Torres a écrit :
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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* A more detailed account of all changes is available in the Apollo ChangeLog: 

* 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 

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

<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

Mailing Address:
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New Apollo Release 2.0.5(JB#9334e76fd)

nathandunn

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

On Jan 5, 2017, at 9:27 AM, Nathan Dunn <[hidden email]> wrote:


On Jan 5, 2017, at 5:22 AM, Loraine Guéguen <[hidden email]> wrote:

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:


via your reported bug:


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


Le 09/12/2016 19:39, Monica Munoz-Torres a écrit :
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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* A more detailed account of all changes is available in the Apollo ChangeLog: 

* 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 

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

<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

Mailing Address:
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New Apollo Release 2.0.5(JB#9334e76fd)

Loraine Guéguen
In reply to this post by nathandunn
Hi,

Is Apollo release 2.0.4 compatible with Java 8 ?

Loraine Guéguen

Le 05/01/2017 18:27, Nathan Dunn a écrit :

On Jan 5, 2017, at 5:22 AM, Loraine Guéguen <[hidden email]> wrote:

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:


via your reported bug:


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


Le 09/12/2016 19:39, Monica Munoz-Torres a écrit :
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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* 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.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

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

<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

Mailing Address:
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New Apollo Release 2.0.5(JB#9334e76fd)

nathandunn
Yes.

Nathan

On Jan 16, 2017, at 3:30 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Is Apollo release 2.0.4 compatible with Java 8 ?

Loraine Guéguen

Le 05/01/2017 18:27, Nathan Dunn a écrit :

On Jan 5, 2017, at 5:22 AM, Loraine Guéguen <[hidden email][hidden email]> wrote:

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:


via your reported bug:


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


Le 09/12/2016 19:39, Monica Munoz-Torres a écrit :
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). 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:

* Detailed, searchable documentation on pre-requisites, configuration, and installation guides found at: 

* 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.readthedocs.io/en/stable/Apollo2Build.html

* Migrating existing annotations: Please find detailed information about migrating existing installations and their annotations at 

* Troubleshooting, GitHub tracker, Mailing List: 
* 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, 

<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

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


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-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
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Place Georges Teissier
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
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/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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