Guruprasad Anada
ee3cddc5df
Replacing \"qual\" datatype with 3 new datatypes: qualsolid, qual454 and qualsolexa.
2009-04-29 11:53:22 -04:00
Greg Von Kuster
11312358a4
Display only the number of associations on the main users, groups, roles pages rather than the associated objects - much faster display times. Also a tweek to my last fix for the column_maker tool.
2009-04-27 16:03:44 -04:00
Guruprasad Anada
55587fdb87
Added an option to mask non-CpG sites to the \"Mask CpG sites\" tool.
2009-04-27 11:59:42 -04:00
Greg Von Kuster
2972b94ab5
Fix for column_maker tool when input dataset has missing or invalid metadata values.
2009-04-27 10:50:17 -04:00
Anton Nekrutenko
871dfe4a6d
Added column info to MB wrapper
2009-04-24 15:06:51 -04:00
Guruprasad Anada
54667b80e6
Bug fixed in linear regression tool, and new option added to grouping tool.
2009-04-21 10:53:34 -04:00
Anton Nekrutenko
309204e5f9
Fixed finf_diag_hits plus a ttypo correction
2009-04-21 09:36:42 -04:00
Guruprasad Anada
6d82e40e41
Updating security from central
2009-04-03 13:31:19 -04:00
Guruprasad Anada
d0c13d7ec4
Added a new option to specify minimum match value in the liftOver tool.
2009-04-03 13:25:01 -04:00
Greg Von Kuster
fb2441caa1
merging heads
2009-03-26 11:13:13 -04:00
Greg Von Kuster
bd41001a99
i18n fix: dataset.info should not be translated since it will generally not have an entry in the catalog. Wormbase fixes: URL to main site corrected, and all supported builds added to gbrowse_build_sites.txt.
2009-03-26 09:34:05 -04:00
Greg Von Kuster
05c2d4222b
merging from central
2009-03-20 03:06:40 -04:00
Greg Von Kuster
354d0447df
Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes.
2009-03-20 02:49:30 -04:00
Greg Von Kuster
c0a4d982aa
merging from central
2009-03-19 21:44:42 -04:00
Greg Von Kuster
ad8f672677
Fixes for wormbase tools, use post as http method rather than get.
2009-03-19 21:41:06 -04:00
Nate Coraor
86eb5e62b2
Asynchronous uploads. Currently disabled in IE, since IE throws
...
occasional 'permission denied' errors when jquery attempts to set the
form target. Compatible with the nginx upload module, but interrupted
uploads will remain in the 'upload' state indefinitely.
2009-03-13 13:48:59 -04:00
Ian Schenck
985f7c63fa
Collapsed changeset: Trackster plugged into galaxy with behind-the-scenes indexing of Wiggle, coverage and interval datasets.
2009-03-11 00:29:01 +00:00
Greg Von Kuster
e55a4d84f8
More library work - requires database schema update:
...
1) include templates in the upload form for library datasets
2) Add user_id column to library_dataset_dataset_association table
3) Add message column to library_dataset_dataset_association table
4) Several miscellaneous bug fixes related to uploading library datasets
SQL commands required:
ALTER TABLE library_dataset_dataset_association ADD COLUMN user_id INTEGER;
ALTER TABLE library_dataset_dataset_association ADD CONSTRAINT library_dataset_dataset_association_user_id_id_fkey FOREIGN KEY (user_id) REFERENCES galaxy_user(id);
ALTER TABLE library_dataset_dataset_association ADD COLUMN message VARCHAR(255);
2009-03-09 17:02:21 -04:00
Guruprasad Anada
25b0fd287e
Commiting changes from central to security.
2009-03-08 14:28:11 -04:00
Guruprasad Anada
280bd8e338
Modified help for \"get Indels\" tool, and made some small changes to the perl script.
2009-03-08 14:25:19 -04:00
Guruprasad Anada
fa533faa95
push changesets to security from central
2009-03-05 13:09:02 -05:00
Guruprasad Anada
ebeece6204
Adding a tiny fix to scatter plot tool.
2009-03-05 13:02:17 -05:00
Greg Von Kuster
987df32669
Fix for rendering tools / workflows in target frames, also elimnate the Workflow link in the tool panel as we're now using the menu bar.
2009-02-23 13:52:34 -05:00
Greg Von Kuster
377a5d8981
Add the Libraries tab to base panel and fix the access_libraries tool config for PrognosysBio.
2009-02-23 11:04:27 -05:00
Guruprasad Anada
6fd54350eb
Integration of Assaf Gordon's Solexa toolkit into Galaxy - (all tools except 3 are working fine).
2009-02-20 14:17:46 -05:00
Anton Nekrutenko
8e6f06d30b
restoring original files
2009-02-10 11:54:53 -05:00
Anton Nekrutenko
1839cde45a
Another typo
2009-02-10 11:31:15 -05:00
Anton Nekrutenko
8624d6c974
Usability tweak for catWrapper
2009-02-10 11:01:54 -05:00
Anton Nekrutenko
f6f3092347
clean up
2009-02-10 10:43:21 -05:00
Anton Nekrutenko
01d16b3883
modified mergeCols to take advantage of repeat tag. Looks foolproof now.
2009-02-10 10:06:17 -05:00
Anton Nekrutenko
19bb2c924c
A simple tool for merging columns. Surprisingly useful for some analyses and also requested by a user lest Friday
2009-02-09 23:57:41 -05:00
Nate Coraor
42cbc8d893
Set a width hint for the library browser
2009-02-06 14:34:57 -05:00
Ian Schenck
28016bd908
Using deprecated sha module in place of hashlib to keep compatibility with python2.4
2009-02-05 15:34:31 -05:00
Daniel Blankenberg
377c2427a7
Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.
...
Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size.
The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.
2009-02-04 14:55:45 -05:00
Guruprasad Anada
7db6a54cf7
updating security from central
2009-02-03 18:36:50 -05:00
Guruprasad Anada
b45b74f3ec
Fixes to get functional tests working.
2009-02-03 18:34:27 -05:00
Guruprasad Anada
a691c492d9
updating security from central
2009-02-03 15:17:00 -05:00
Guruprasad Anada
41d1ce79c8
Removed lzo requirement from two tools- getIndels and qualityFilter.
...
Also added validator to the regression tools.
2009-02-03 15:06:21 -05:00
Nate Coraor
f8ce6fc19d
merge
2009-01-30 11:39:29 -05:00
Nate Coraor
288d581b75
Fix annotation profiler interpreter to be python, not python2.4
2009-01-30 11:37:51 -05:00
Ian Schenck
937e568e19
Ironed out nasty exceptions thrown on invalid genetrack outputs. Still need a way to resolve the optional 2nd output (exported intervals), and ensure the user picks at least 1 coverage dataset or 1 feature dataset.
2009-01-27 17:10:30 -05:00
Guruprasad Anada
753c5466c1
Commit changes from central to SEcurity
2009-01-27 16:20:13 -05:00
Guruprasad Anada
1f62ffbb01
Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools.
2009-01-27 16:17:22 -05:00
Nate Coraor
4f02a56abc
merge
2009-01-27 14:49:21 -05:00
Daniel Blankenberg
4279415d2a
Fix For MAF Filter tool.
...
Looks like when grouping parameter types were updated to be recursively wrapped properly, this tool was not updated.
2009-01-26 14:48:45 -05:00
Nate Coraor
de2fff1df2
merge
2009-01-23 12:57:06 -05:00
Anton Nekrutenko
076398c821
Changed grouping output to tabular
2009-01-22 12:46:37 -05:00
Anton Nekrutenko
43891dced2
updated bar charter to use png instead of pdf
2009-01-22 12:06:29 -05:00
Greg Von Kuster
bb2b948557
merging from central
2009-01-22 08:51:48 -05:00
Greg Von Kuster
705994a0fc
Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version.
2009-01-22 08:50:52 -05:00
Guruprasad Anada