We are pleased to announce the latest Apollo release Apollo 2.0.5 Some of the new features include:
Some important bug fixes:
* 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.rea * 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/use * 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/dem * These and more details are available at the Apollo Website and the Apollo repository. We look forward to your questions and suggestions. Sincerely, ![]() 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. |
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]
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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 :
-- 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. |
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.
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
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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
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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 :
-- 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. |
Yes. Nathan
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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