dbfe147df7
Fixed bug that was causing problems in UCSC Archaea tool.
2007-06-27 16:00:47 +00:00
a7336bfaa5
Support for Gff version 3 which will be coming from GMOD applications (wormbase, hapmap, etc).
2007-06-26 15:43:57 +00:00
1e8c4155bf
add one more option for run_functional_tests.sh: listing all the ids
2007-06-22 15:25:14 +00:00
0baf801408
Require history id of dataset inorder to launch an asynchronus tool.
2007-06-20 15:22:54 +00:00
4919d2d048
Adding new tool "Extract features from GFF file" under Fetch Sequences and Alignments section.
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Have not been able to get this tool to pass functional test as test support with the new conditional constructs is yet to be worked out.
2007-06-19 14:04:41 +00:00
e7b15fa019
Fixes for BioMart and Subtract Query and another example for Filter.
2007-06-18 20:23:50 +00:00
a1c3641247
modify: (add) testing one tool and one case
2007-06-18 18:09:55 +00:00
1ad9a5d09e
Adding a backref to the dataset->children relationship so that setting the
...
parent attribute is pushedto the database (importing histories with children
now works correctly).
2007-06-18 18:05:26 +00:00
efdf899e60
Fix history import for histories with nested datasets.
2007-06-18 17:26:02 +00:00
f3697bb533
Some fixes wrt datatypes stuff (interfaces.root.copy_dataset was broken which
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breaks a variety of other things)
2007-06-18 16:58:55 +00:00
418d3313dd
Fixes to asynchronous connections, such as encodeDB.
2007-06-15 16:52:53 +00:00
48a69153b1
rollback
2007-06-15 15:59:25 +00:00
217dedf742
Incremental metadata commit. I feel like I'm doing something wrong here but don't know what. It just feels too complicated or something. Input?
2007-06-14 15:53:01 +00:00
b68986d1e4
Initial metadata commit. The framework is there, need to figure out what to do with it now and add unit tests
2007-06-08 17:16:35 +00:00
cc707c521e
Oops! Forgot to add the example image files for flanks tool.
2007-06-08 15:54:56 +00:00
b684baba08
Enhancements to 'Get flanks' tool based on Dr. Gilmour's requests.
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The tool now allows the user to offset co-ordinates and get flanking regions around start and end co-ordinates separately.
2007-06-08 15:46:36 +00:00
7a692f610c
Fixed a bug introduced when restored saving command_line to job table.
2007-06-07 15:27:59 +00:00
89c676382c
More complete use of nested contexts in 'update_state', should fix another
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problem noted by Guru.
2007-06-04 21:41:23 +00:00
f597208b13
change test parameter
2007-06-04 18:41:54 +00:00
063e6ebb54
update test dat for nj_tree_newick tool
2007-06-04 18:39:41 +00:00
ef341615a9
change test parameter: allow partial blocks(maf_to_fasta_multiple_sets.xml)
2007-06-04 16:14:34 +00:00
4dbd6b603d
update test data, cf_maf2fasta.dat
2007-06-04 16:12:01 +00:00
30bbb3c1c1
remove tool show_in_ucsc
2007-06-04 14:21:10 +00:00
a6d5eaa93f
rollback. sorry, removed the wrong files
2007-06-04 14:18:13 +00:00
251b052221
remove tool build_ucsc_custom_track
2007-06-04 14:11:53 +00:00
250c3a3eb9
add some data
2007-06-04 13:53:22 +00:00
19f1bd4ace
change test data to smaller ones
2007-06-02 03:06:00 +00:00
ba95acc6a4
remove useless data
2007-06-01 20:53:43 +00:00
38128dd7aa
change test data to smaller ones
2007-06-01 20:15:01 +00:00
c82bce21d5
Temporary patch to allow edit to mangle stuff that has no column metadata and is not an interval. This should all be temporary stuff to get us through until metadata is done.
2007-06-01 19:30:50 +00:00
4cbfce361b
Add the ability to define datatypes in the configuration file.
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Datatypes are defined like:
[galaxy:datatypes]
bed = galaxy.datatypes.interval:Bed
png = galaxy.datatypes.images:Image,image/png
where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
2007-06-01 19:25:19 +00:00
437399fc66
Added expression validation for column_maker, filter.
2007-06-01 14:31:13 +00:00
76d525e694
Re-saving command_line in the job table for reporting purposes.
2007-06-01 12:35:09 +00:00
77f1195f7a
Changed trans->app.
2007-05-31 20:31:28 +00:00
07257f2670
Fix for Summary Statistics (oops, indentation bug!!!)
2007-05-31 19:33:32 +00:00
6d680f95f3
Big change in JobWrapper.prepare. Trans is no longer available, so app is going to be passed instead. None of the existing tools use trans so this is ok, although they do 'refer' to it. Going to change that to hopefully avoid future pitfalls.
2007-05-31 19:32:18 +00:00
aa1b320baf
Fixed up the "contexts" used to look up variables in parameter grouping
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constructs. You can now reference and parameter value defined on a previous
page or in a higher level group. Should fix a problem Guru found.
2007-05-31 19:02:37 +00:00
da3ca1cf77
Fixed error catching the the exec_after_process hook for operations. Previously it would NEVER set job state to error. Now it sets job state to error if there is stderr.
2007-05-31 15:39:48 +00:00
ab162d938a
Operations now won't fail on bad data. It skips the lines and tells the user about it. There is a possibility of getting a traceback from python though, along with data in the file, which won't change the job state to ERROR. How is this accomplished? Oh yeah...closes out ticket 135.
2007-05-30 21:07:33 +00:00
93170329b8
Fix for EMBOSS:fuzznuc. Update command line args from version 3 to 4.
2007-05-30 17:46:37 +00:00
7ab8bb1450
Corrected typo in tool name and enhanced error messages.
2007-05-30 17:33:20 +00:00
be673c2a5a
There has to be at least one tool named 'ucsc_proxy' for the proxies to work. They all use the same code with different urls, but they have to submit back to the tool_runner at the end. This closes ticket 121.
2007-05-30 15:47:59 +00:00
ca9b09487c
Fix for EMBOSS:primersearch. This resulted from a change in command line parameters from EMBOSS version 3 to 4.
2007-05-30 14:36:09 +00:00
d486a36f1b
typo
2007-05-30 03:29:18 +00:00
b79b94363c
Unsequenced genome for june and some welcome page clean up
2007-05-30 03:27:01 +00:00
d846a2f30c
I need to make svn auto grep for print statements before committing, this is embarrassing.
2007-05-29 22:02:49 +00:00
9c26582b9f
Added the ability to map hooks to different functions. Did away with sys.path mangling and module hell. Cleaned up operations to take advantage of the changes.
2007-05-29 22:00:57 +00:00
c6d4171559
Decode keys as well in tool parameters. (Aiyeeee, this is all for buggy old psycopg)
2007-05-29 21:08:44 +00:00
3ad0ee0f1f
Added a configuration parameter.
2007-05-29 20:51:51 +00:00
b6d8217d74
Hmmm... not so intuitive...
2007-05-29 20:43:33 +00:00
Greg Von Kuster