Guruprasad Anada
0e29e97366
Committing changes to 'extract genomic dna' tool - twobit file will be opened only once per job. (Courtesy: Gordon).
2009-07-20 16:57:55 -04:00
Daniel Blankenberg
cc22aee3cb
Initial pass at allowing the setting of certain metadata parameters on upload (controlled via a flag). This allows the user to specify the 'base_name' to be used for Rgenetics datatypes, etc. Bunch of cleanup needed in upload.
2009-07-15 14:11:35 -04:00
Guruprasad Anada
15652612b7
A bug fix for extract genomic dna to handle invalid chromosomes correctly.
2009-07-07 12:06:35 -04:00
Guruprasad Anada
004b6cbd01
A tiny bug fix for Sort tool - the delimiter is now defaulted to tab.
2009-06-25 15:34:05 -04:00
Guruprasad Anada
018537baf6
Extract genomic DNA tool now uses only alignseq.loc to access sequence files. The twobit.loc file will henceforth be unnecessary, and all sequences from it should be moved to alignseq.loc.
2009-06-25 15:29:24 -04:00
James Taylor
db9c0a9870
Commenting out 'other dbkey' in upload
2009-06-11 15:41:57 -04:00
James Taylor
537f8952ef
Merging Ian's trackster update with current head
2009-06-11 12:20:03 -04:00
Daniel Blankenberg
7c712f59a1
Fix missing split/join char in Join tool when filling nonjoined columns.
2009-06-10 11:58:21 -04:00
Daniel Blankenberg
c0d797e00d
Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged.
...
A more structured way of storing these files (rather than dumping in a directory) is worth considering.
2009-06-08 12:49:26 -04:00
Greg Von Kuster
49938abb76
Add EuPathDb data source tool config.
2009-06-01 10:27:04 -04:00
Guruprasad Anada
167ce59b29
Bug fixes for histogram liftover and grouping tools.
2009-05-29 11:07:18 -04:00
Greg Von Kuster
a9cd544be9
Add a defaulttimeout setting of 10 minutes to the urlopen() call for requests to remote data sources.
2009-05-28 11:10:44 -04:00
Greg Von Kuster
e608f904ee
Add tool config for GrameneMart data source.
2009-05-27 14:19:59 -04:00
Daniel Blankenberg
f3658d8fa9
Add the ability for the tabular join tool to fill in empty columns.
...
Working tests are needed.
2009-05-14 12:55:14 -04:00
Guruprasad Anada
24293166da
MAQ mapping pipeline for SOLiD data
2009-05-13 21:54:45 -04:00
Guruprasad Anada
4f1a6fe60f
Added SOLiD tool section with QC tools.
2009-05-05 22:44:30 -04:00
Guruprasad Anada
f546868cf5
A tiny bug fix for linear regression tool.
2009-04-30 11:07:34 -04:00
James Taylor
cff01df993
Accidently commited a testing change, removed
2009-04-29 14:47:18 -04:00
James Taylor
139a30e964
Handle the addition of new tool parameters better in the workflow editor. Default values will be filled in and a message displayed to the user
2009-04-29 13:46:02 -04:00
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
Ian Schenck
3c6fc67c88
Missed adding chrominfo.py, due to my hardcoded paths in test environ. Should be good now?
2009-04-23 14:42:35 -04:00
Ian Schenck
feda672ffa
- Performance of indexers much improved.
...
- 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.
2009-04-23 13:46:52 -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
Guruprasad Anada