Merge branch 'master' of https://github.com/GMOD/Apollo

ChangeLog.md

@@ -1,7 +1,41 @@
 
+## 2.0.7
+
+Features
+
+- Allow setting of alternate translation table per organism using the _Details_ panel under the _Organism_ tab in the Annotator panel. [#95](https://github.com/GMOD/Apollo/issues/95)
+- Draggable BAM tracks now support coloring by strand. Reads aligned to forward strand are colored blue, while those in the reverse strand are red.  [#412](https://github.com/GMOD/Apollo/issues/412)
+- The list of _Tracks_ in the Annotator panel now allows for the separation of data types into categories. [#536](https://github.com/GMOD/Apollo/issues/536)
+- When applicable, warnings now alert users of insufficient permissions to perform certain functions. [#553](https://github.com/GMOD/Apollo/issues/553)
+- Restrictions are now in place to prevent users from modifying or deleting annotations that they did not create. [#1260](https://github.com/GMOD/Apollo/issues/1260)
+- Updated settings for the ability to filter by organism when applying metadata. For instance, admin may now apply canned comments, keys and values, only to a subset of organisms in their server. As well, statuses can be retrieved per type of genomic element, per organism, etc. [#1676](https://github.com/GMOD/Apollo/pull/1676)
+- Admins can now build public URLs to hyperlink directly to a specific genomic element. [#1482](https://github.com/GMOD/Apollo/pull/1482)
+- It is now possible to set _Statuses_ as well as adding or editing _Canned elements_ using our Web Service (REST) API. [#1538](https://github.com/GMOD/Apollo/pull/1538)
+- In the absence of ```Name``` attribute in GFF3 file, Apollo uses ```ID``` attribute to name the annotation in JSON. [#1639](https://github.com/GMOD/Apollo/pull/1639)
+- A number of other improvements to performance have been made, such as fetching preferences from session. [#1604](https://github.com/GMOD/Apollo/pull/1604)
+- Added documentation for a Web Service wrapper for Python, PHP, etc. See [Web Services API documentation](http://genomearchitect.readthedocs.io/en/latest/Web_services.html).
+
+Bugfixes
+
+- Fixed bug in which ```add_transcripts_from_gff3_to_annotations.pl``` replaced valid mRNA name with gene name. [#1475](https://github.com/GMOD/Apollo/issues/1475)
+- Fixed bug in which ```REMOTE_USER``` was not cached everywhere and was being ignored on ping request. [#1492](https://github.com/GMOD/Apollo/pull/1492)
+- Added warning to Production pre-requisites: if using gradle and gradlew, admins should define ```JAVA_HOME``` to avoid build fails. See documentation [here](http://genomearchitect.readthedocs.io/en/latest/Setup.html#production-pre-requisites).
+- Fixed sorting bug on the dropdown list of organisms. [#1497](https://github.com/GMOD/Apollo/issues/1497)
+- Fixed a bug in which the absence of an organism created downstream issues such as errors listing groups of users in Annotator panel. (Feature for admins). [#1504](https://github.com/GMOD/Apollo/pull/1504)
+- Fixed a bug in which creating a user via Web Service API generated an error message. [#1510](https://github.com/GMOD/Apollo/pull/1510)
+- Fixed import script ```add_transcripts_from_gff3_to_annotations.pl``` to introduce correct handling of sequence alterations and read-through stop codons. [#1524](https://github.com/GMOD/Apollo/pull/1524)
+- Fixed bug that now allows leading start non-M codons in organisms with non-standard code to be translated as Methionine (M). [#1544](https://github.com/GMOD/Apollo/issues/1544)
+- Updated GWT code to fix a bug that prevented Apollo from generating URLs appropriately - pipes were not being encoded. [#1606](https://github.com/GMOD/Apollo/pull/1606)
+- Fixed bug in the calculation of open reading frames for the negative strand for the purpose of coloring each exon according to the CDS. Exported sequences had been - and remain - correctly generated. [#1629](https://github.com/GMOD/Apollo/issues/1629)
+- Fixed bug that delayed propagation of updates when boundaries for an annotation's parent element were changed. [#1631](https://github.com/GMOD/Apollo/issues/1631) 
+- Restored _'Pin to top'_ and _'Delete track'_ functionality for tracks with ```HTMLFeatures```. [#1632](https://github.com/GMOD/Apollo/issues/1632)
+- Fixed cascade bug when changing annotation type for an annotation that has a read-through stop codon. [#1717](https://github.com/GMOD/Apollo/pull/1717)
+
+
 ## 2.0.6
 
 Features
+
 + Moved the native track panel button to the main window #1398
 + Add new 'default_group' param for remote_user auth #1445
 + Added icon to toggle view of native JBrowse tracks that is always visible #1452

docs/Configure.md

@@ -144,26 +144,22 @@ jbrowse {
 
 The default translation table is [1](http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1) 
 
-To use [one of the others](http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) set the number in the ```apollo-config.groovy``` file as:
+To use a different table from [this list of NCBI translation tables](http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) set the number in the ```apollo-config.groovy``` file as:
 
 ```
 apollo {
 ...
   get_translation_code = "11"
 }
-```
-
-These correspond to the NCBI translation tables.   
+```   
 
-To add a custom translation table, you can add it to to the ```web-app/translation_tables``` directory as:
+You may also add a custom translation table in the ```web-app/translation_tables``` directory as follows:
 
 ```
 web-app/translation_tables/ncbi_customname_translation_table.txt
 ```
 
-and specify the ```customname``` as:
-
-In apollo-config.groovy:
+Specify the ```customname``` in apollo-config.groovy as follows:
 
 ```
 apollo {
@@ -172,6 +168,9 @@ apollo {
 }
 ```
 
+As well, translation tables can be set per organism using the _'Details'_ panel located in the _'Organism'_ tab of the Annotator panel in the Apollo window: to replace the translation table (default or set by admin) for any given organism, use the field labeled as _'Non-default Translation Table'_ to enter a different table identifier as needed. 
+
+
 ### Logging configuration
 
 To over-ride the default logging, you can look at the logging configurations from