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Author SHA1 Message Date
Daniel Blankenberg a19ae79b85 Change color space FASTA file type from fastqsolid to fastqcssanger. 
Cripple accepted tool input formats for many of the FASTQ tools to only allow only fastqsanger and fastqcssanger to be used.
 2010-03-02 10:47:23 -05:00
Jeremy Goecks fa9367ed72 Fix bug that prevented tags with capital letters from being deleted. 2010-03-02 09:51:05 -05:00
Nate Coraor 9a8c5f6711 psycopg2 scramble fix 2010-03-02 00:38:57 -05:00
James Taylor 31a4f80604 [mq] workflow-invocation: Track workflow invocations in database, provide a view of the history grouped by workflow and job 2010-02-11 00:17:04 -05:00
Kanwei Li ab11e28bce Fix uploads not working 2010-03-01 17:47:28 -05:00
Greg Von Kuster 3aa2fc3601 Passwords are no longer changed ( sanitized ) as part of processing the request. Enhanced functional tests to cover the scenario where passwords include chars that break in sanitization. 2010-03-01 16:07:54 -05:00
Nate Coraor 2db1dbc5a9 update GeneTrack egg 2010-03-01 16:00:26 -05:00
Nate Coraor 006716f53a Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES 2010-03-01 15:41:30 -05:00
James Taylor a33a746dd8 UI tweaks 2010-03-01 13:30:37 -05:00
James Taylor a5f6a3dfb0 Page editor: use Galaxy styles for drop downs in menubar 2010-03-01 12:46:54 -05:00
James Taylor 4b4178c643 Ran optipng on sprite images 2010-03-01 12:14:04 -05:00
James Taylor ae1167251e fix: menu border opacity 2010-03-01 12:09:38 -05:00
James Taylor c99f487f5f 1) Jquery 1.4 again, with fixed tooltips; 2) Style changes for history, icons and editable text areas. 2010-03-01 12:01:50 -05:00
Jeremy Goecks b1a90dc158 Clean up pages: 
-remove unused code;
-show annotation field when creating a page;
-fix bug when filtering pages by sharing status.
 2010-02-28 22:19:56 -05:00
Kelly Vincent d091640cb5 Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass 2010-02-25 23:20:19 -05:00
Ramkrishna Chakrabarty 300b34494c lims: bar code related state change bug fixed 2010-02-25 14:59:43 -05:00
Nate Coraor 0bfa58679b Fix locations of cached data for tests 2010-02-25 12:27:07 -05:00
Ramkrishna Chakrabarty 3df11a4257 lims: deactivate the enter key in requests page so that the scanner can be used to enter barcodes for each sample 2010-02-25 11:28:14 -05:00
Kanwei Li d64501f412 Fix workflow bug where "Layout" changes would not be saved, and "Save and Close" did not save 2010-02-24 18:55:30 -05:00
Daniel Blankenberg 77c4785eb7 Update Combine FASTA and QUAL tool to allow the quality score file to be optional. 
When not provided, the output will be fastqsanger or fastqsolid (when a csfasta is provided) with each quality score being the maximal allowed value (93).
 2010-02-24 16:50:06 -05:00
Daniel Blankenberg f11e459fbd Update test framework to allow not setting a value for optional DataToolParameter inputs. 2010-02-24 16:48:22 -05:00
Nate Coraor 6e9996f89a Fix for set metadata tests when setting metadata externally 2010-02-24 15:54:52 -05:00
Daniel Blankenberg 1dcf92edde Move FASTA classes in galaxy_utils from fastq.py to fasta.py. 2010-02-24 11:57:35 -05:00
Ramkrishna Chakrabarty 6b45a2c1f9 lims: 
- code cleanup
- cleanup tmp files after data transfer
 2010-02-24 10:42:36 -05:00
Ramkrishna Chakrabarty dd4757f20a lims: 
- added error msg when dataset transfer is started for samples with no library
- fixed typos
- now dataset transfer does not affect sample state
- request completion logic restored.
 2010-02-24 10:04:03 -05:00
Kelly Vincent d0e44fe520 Adding missing sam_merge test files 2010-02-24 08:44:22 -05:00
Kelly Vincent 09fa3f0bf1 Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools. 2010-02-24 07:11:43 -05:00
Daniel Blankenberg a28313bb46 FASTQ Manupulation tool no longer considers @ when matching or translating sequence identifiers. 2010-02-23 23:17:09 -05:00
Daniel Blankenberg 4cb98d8b5f Add gnuplot requirement tag to boxplot tool. 2010-02-23 19:54:54 -05:00
Kanwei Li e555f74b3b Refactor grid_base.mako and Fixes #285 2010-02-23 17:58:44 -05:00
Daniel Blankenberg 8082c6f36f Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid. 
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)
 2010-02-23 16:48:07 -05:00
Nate Coraor ea7f5879e1 update buildbot_setup.sh for new data location 2010-02-23 16:12:20 -05:00
Nate Coraor 5e34e82e5c Modify functional_tests.py to allow for testing of an environment nearly identical to Galaxy Test/Main via buildbot 2010-02-23 15:14:28 -05:00
Kelly Vincent a314b3716b Updated BWA wrapper, SAM to BAM, SAM Merge, and SAM Pileup so that the return code of the program is captured and if it fails, the stderr is printed; temp files are created locally; a message is printed if results file empty. 2010-02-23 10:40:19 -05:00
Guruprasad Anada f47cd6a27f Bug fixes to LCA tool 2010-02-22 16:22:12 -05:00
Jeremy Goecks 7e96a18c68 Annotations for published items: (1) added annotations to pages; (2) added annotation column to all published item grids; (3) refactored annotation code out of base controller and into its own mixin. 2010-02-22 13:56:51 -05:00
Greg Von Kuster 9d7974a3cb Fix for displaying datasets in the bx browser. 2010-02-22 09:21:42 -05:00
Jeremy Goecks 1d5f5e89f5 Make anchor ID/name editable in pages. 2010-02-22 08:12:03 -05:00
Jeremy Goecks 04ff53c4de Pack script. 2010-02-22 07:43:12 -05:00
Jeremy Goecks d752edcae0 Added functionality for creating links on pages: (1) existing links are editable and (2) can create in-page, named anchors. 2010-02-22 07:42:07 -05:00
Kanwei Li 51c7ec8fb3 trackster: 
- Refactor
- Focus on new browser text
- Fixed linetrack bug when switching chroms
 2010-02-19 17:54:44 -05:00
Nate Coraor bb6a16d1f4 Fix MySQL_python static egg on OS X 2010-02-19 14:34:25 -05:00
Jeremy Goecks f5f52bd419 Fix bug so that, when a user submits edits to a page's attributes, he is redicted to his page list. 2010-02-19 11:29:25 -05:00
Greg Von Kuster 9ebc5cfdba Re-fix new functional test support for setting check boxes and boolean tool params to false, and fix a broken functional test in the security and libraries suite. 2010-02-19 10:01:33 -05:00
Ramkrishna Chakrabarty 740e73b5e9 lims: 
- added data directory field in sequencer info
- UI changes on samples page
 2010-02-18 21:38:49 -05:00
Jeremy Goecks 6d3aa1fe7b Make page 'View' option use same URL as shared/accessible/published page does so that relative URLs behave the same in both contexts. This change addresses the issue raised by the temporarily broken hyperlink on the Bushman page. 2010-02-18 17:04:43 -05:00
Ramkrishna Chakrabarty 650590cd5e lims: added feature to to transfer folders from a sequencer 2010-02-18 11:50:19 -05:00
Guruprasad Anada 20bb7f6d5b Added mm5 to the list of manual builds 2010-02-18 11:26:39 -05:00
Greg Von Kuster a8e265fc31 Fix CheckboxField.is_checked(), which was broken if change set 3373. 2010-02-18 09:47:21 -05:00
Greg Von Kuster 05433e9315 Fix bug introduced in change set 3408:6471c9b8149c when testing form fields with labels / values longer than 30 chars. 2010-02-17 16:37:02 -05:00