Provides two links for IGV:
1) web - to view with Java web start IGV if the user has no IGV installed
2) local - to view in the user's running IGV instance (requires remote port enabled in IGV)
- Fix track preferences not being applied
- Fix chroms not being selectable when a new track browser is created
- Fix ReferenceTrack not working with filters
- Fix visual analytics error when tool configuration has changed
More work is required to allow the one-off indexes built by bowtie to become Galaxy datasets; alternatively, the custom genome selection could be limited to the index datatype for input (and not allow fasta directly), which would allow implicit datatype conversion to occur when a fasta file is selected as input, but this would prevent the index tuning that is currently available when currently selecting a fasta file.
- New summary tree data structure that specializes in aggregation at defined levels
- BED converter for summary_tree
- Feature tracks now have a summary display when there are a lot of things to be rendered on screen, but will display simple lines and full detailed view as you zoom in and can fit more on screen
- Added option to display number of features in a region of summary view
- Line tracks can now be displayed as intensity
- Pack scripts
- Use new array_tree summary structure. Feature tracks now display as intensity graphs at higher levels, and switch to detail levels when they fit the screen well
- Create array_tree indices for bed format to support the above (bam still in progress)
- Other fixes and improvements, including new icons
Add the ability for display applications to be populated dynamically based upon the content of (e.g. tabular) files.
Display application links can be filtered by various attributes, including e.g. dataset dbkey matching from field in a file or an attribute matching a Galaxy application configuration setting.
Param and Data URL values can now be generated dynamically, allowing e.g unique base filenames to be created and used.
See updated xml configurations in /display_applications/ for examples of syntax.
Tools include:
FASTQ Groomer convert between various FASTQ quality formats
Combine FASTA and QUAL into FASTQ
FASTQ joiner on paired end reads
FASTQ splitter on joined paired end reads
FASTQ to FASTA converter
FASTQ Summary Statistics by column
Filter FASTQ reads by quality score and length
FASTQ Trimmer by column
Manipulate FASTQ reads on various attributes
Boxplot of quality statistics (Generic, with outliers)
Applications are assigned to specific datatypes (i.e. on an extension basis) via the datatypes_conf.xml file.
View the sample display applications at /display_applications/[ucsc/]*.xml for examples of usage.
Provided sample display applications:
View BAM files (with bai indexes) at UCSC using BigDataUrl support.
ucsc interval as bed viewer - not enabled by default (the old style display app is still used by default; both can be used simultaneously - but this would likely be confusing)
GeneTrack viewer - any interval datatype can now be viewed at GeneTrack, if the application is enabled for a particular datatype; also a valid display application for genetrack datatype.
Display applications can make full use of datatype converters, even allowing explicitly defined multi-step conversions, e.g. interval --> bed --> genetrack; the datatype conversion framework will need to be enhanced to natively support multi-step conversions before this can be done implicitly.
A new datatype, bedstrict, has been defined, the only way to have an item with this datatype is to be created by a tool; metadata cannot be edited; and sniffing this datatype would require aggressively parsing the entirety of the file. A bedstrict file must conform exactly to the BED specification (whereas Galaxy allows BED files to have non-standard columns). These files are suitable e.g. for display at the UCSC genome browser and is used by the new ucsc interval display application.
Add a bed to bedstrict converter, this is used by the ucsc interval display application.
Add a bed to genetrack converter, this is used by the new GeneTrack display application. TODO: If the GeneTrack indexer can be enhanced to accept column assignments, this should be an interval to genetrack converter.
Several performance enhancements available for the ucsc tools, such as bigurl support, potential speed improvement when loading a user's history than the old style for certain displays, e.g. ucsc interval display no longer requires the viewport (position) to be calculated for each relevant history item in a users history; this calculation now occurs on a separate page after the user clicks a view link. Non-strict BED files no longer have their content calculated on the fly and then streamed, etc.
Refer to additional comments in code.
- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types
- Indexing for tracks done in background with a visual treatment done to Trackster
- DB builds can be uploaded by a user (chromInfo/len extension).
- TODO: Add ability to change the dbkey of a dataset to any arbitrary string value.
Kanwei Li