June 21, 2010 New Development News Brief
Here are the highlights of what you will get if you perform the following upgrade:
hg pull -u -r 4cdf4cca0f31
Existing Feature Improvements
- Security fixes for data libraries. Some parameters were not validated, which could allow access to administrative functions without having required privileges.
- Do not allow the dataset file to be removed from disk via the cleanup_dataset.py script for datasets uploaded to a library where the file is not copied into Galaxy's default file location.
- Changes to browse library UI: 1) use standard popup button styles, 2) Move library wide actions out of table header and into manage-table actions.
Add MafCustomTrack datatype and a UCSC external display application which can be used to view this datatype at UCSC.
- Enhance change datatype action in edit attributes form to set metadata externally when so configured.
- Fix a bug with external metadata that caused every dataset association for a particular base dataset to enter the setting_metadata state when metadata was set for one dataset association.
- Fix for datasets getting stuck in setting_metadata state when using external metadata and there was a job failure (e.g. cluster error).
- Added colon as a delimiter for 'Convert delimiters to TAB' tool.
- Update tool_conf.xml.* to only use the generic python FASTQ to FASTA converter by default.
- Add GFF support to GOPS intersect tool.
- Fixed handling of alignments with CIGAR strings with multiple indels for SAM indel filter.
- Change language and parameter names in GOPS subtract to imply that any interval files can be used as input, not just BED files.
- Patch to upload.py for composite file uploads where the user supplies URLs for components. At present, the path for each component is passed as a URL and there's no upload type for composite file components, so this temporary fix searches for :// in the path to figure out if this is a URL upload.
- Add a VCF to MAF Custom Track converter tool. This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers. This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis. Unknown nucleotides are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.
- Fixed a bug in 'Fetch closest features' tool that prevented fetching of immediately adjacent features.
- Fix options bug in cufflinks wrapper.
- Fix for rerun action when a tool is not loaded.
- Add tool searching functionality using Whoosh and lots of jQuery. Search is currently hidden by default but will soon be a user preference.
Functional test harness
- Fix for kcca, linear regression and get indels tools - use 're_match' to accommodate sign and decimal precision changes in kcca output.
- UI enhancements to the remote file browser, double click to open folder.
- Data transfer folder name now includes the date.
- Fix: the data transfer module now works for file/folder names with spaces in them
- Update trackster dataset filter so that only datasets that are not deleted, not from deleted histories, and are in 'OK' state are available for visualization.
- Fix creating new trackster viz, fix autocomplete grouping by first character.
- Supports display of reference sequence in twobit format. Mapping of dbkey to twobit file is done in tool-data/twobit.loc. Reference track will automatically be shown when zoomed in if the twobit file exists for that dbkey. Also fixes a drawing issue with Reference/Read tracks.
- Fixed a sorting bug in the grid framework. Sorting preferences were not getting preserved.
- Fix grid initialization bug that was preventing visualization grids from working properly.
Add the "all" option to the grid's StateColumn.
- Remove the user round robin scheduling policy (it didn't work as intended). The former job_scheduler_policy config option now has no effect.
- Post job action database setup.
- Fix bug in root.history_item_update caused when a tool has been removed.
- Added annotations to run workflow display. New feature: actions in workflow steps. Change name, hide dataset, change datatype enabled.
- Len datasets for custom dbkeys now don't need a history and this fixes an issue with extract workflows.
Fix for double UnvalidatedValue wrapping when extracting a workflow from a history that was created using UnvalidatedValues (e.g. when dynamic options is used in a tool before metadata is ready).
- Fix for extracting a workflow from a history when a tool is not loaded.
- Fix bug that prevented 'All workflows' link from being shown when tool search is active.
- Enhance workflow editor to work with a list of output formats instead of only one. This fixes the bug where outputs utilizing a change_format tag could not be connected to an input that was of the changed-to type.
- Fix for extracting workflows from a history that has a dataset in the error state.
- Add a user_id column to the job table to decouple jobs from sessions.
- When filtering on the state of jobs in the advanced search box in the jobs reports, you now have an "all" option.
- Jobs displayed in the jobs reports are now all color coded by job state.
- Rewrite the jobs report queries to no longer join the job table to the galaxy_session and galaxy_user tables, just join galaxy_user since we now have a direct relation to that table.