Guruprasad Anada
3520ce3aec
Updating security from central
2008-09-24 18:22:55 -04:00
Guruprasad Anada
0f1130e84a
Adding tools to fetch microsatellites and estimate their mutabilities.
2008-09-24 18:20:39 -04:00
Greg Von Kuster
44bc594079
my message
2008-09-22 10:39:47 -04:00
Greg Von Kuster
b4890c1bbb
Integrate with intermine ( data source ) and epigraph ( data destination ). Receiving data from epigraph coming soon. Data is sent to epigraph using a combination of DATA_URL and REDIRECT_URL tool params. This tool creates jobs, but does not queue them for execution.
2008-09-22 10:36:34 -04:00
Guruprasad Anada
e2f4f46a75
Adding tools to compute Substitution rates.
2008-09-21 17:36:28 -04:00
Guruprasad Anada
cb74e79f21
Adding a new set of toolss to perform multiple linear regression analysis.
2008-09-20 18:14:24 -04:00
Wen-Yu Chung
fd1a49f9fe
Fix a bug in shrimp_wrapper and add a tool to split paired-end reads.
2008-09-19 12:42:26 -04:00
Wen-Yu Chung
07118387a1
Fix a bug in shrimp_wrapper and add a tool for splitting paired-end reads.
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Update datatype/fastqsolexa so the number of sequences is correct.
2008-09-19 12:02:13 -04:00
Guruprasad Anada
e53c5a15a3
Updating security from central
2008-09-17 17:25:17 -04:00
Guruprasad Anada
6b68878aec
Forgot to update tool_conf.sample with the new tool details.
2008-09-17 17:14:59 -04:00
Wen-Yu Chung
e7c4d75b34
add SHRiMP mapper for short read tools
2008-09-15 15:18:28 -04:00
Wen-Yu Chung
bca6ad57e1
add SHRiMP mapper for short reads analysis.
2008-09-15 15:04:41 -04:00
Nate Coraor
ffd0be5a3a
Merged from central.
2008-09-12 15:16:38 -04:00
Anton Nekrutenko
74d5327978
Lastz with additional short read changes
2008-09-12 15:14:20 -04:00
Nate Coraor
4edc6d6626
Spiffy new library browser interface. Also, dim datasets in your
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history on which you don't have permissions.
2008-09-10 10:10:13 -04:00
Daniel Blankenberg
da0b09039c
Initial check in of library functionality.
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The ui is Very rough, at best.
Libraries can be accessed by users through a new tool under datasources.
Libraries can be created and accessed for modification via a link on the admin page.
Currently, all library datasets are currently associated with the public group.
Tags have been defined (tables and mappings) and can be associated with a dataset or a folder, but there is currenty no interface for displaying or creating these.
Creation and editing of a library should be an admin only function, however this check is not currently present.
The creation/editing page for a dataset is currently hard coded, it should be dynamic (i.e. datatypes and dbkeys)
Brief description of a library:
A library is composed of a name, description and a root folder.
A folder is composed of a name, description, and a parent folder (none when is the root), where a folder can have many or none child folders and datasets.
A library dataset is composed of most of the same attributes as a history dataset, but it is linked via a folder_id to a folder (instead of a history_id to a history).
Ordering of the library is maintained by the 'order_id' attribute of each folder and dataset object (which is populated by the item_count attribute of a folder)
2008-08-12 16:56:26 -04:00
Greg Von Kuster
666de20b4d
Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.
2008-06-09 20:15:04 +00:00
Greg Von Kuster
1a23f9e55d
Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.
2008-05-29 19:12:36 +00:00
Greg Von Kuster
051dc9ca94
A bit of cleanup, added FASTQ to FASTA converted to tool_conf.xml.sample.
2008-05-27 19:59:33 +00:00
Greg Von Kuster
c32f87624f
Added code for integration with C. Elegans / GBrowse test server.
2008-05-12 18:55:48 +00:00
Greg Von Kuster
185b4353c2
Deleted findcluster_mysql tool code.
2008-05-01 17:44:56 +00:00
Anton Nekrutenko
a3ee9be735
More clean up and modification of FASTA tools
2008-04-29 14:36:04 +00:00
Greg Von Kuster
5657e61320
Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.
2008-04-25 13:04:55 +00:00
Daniel Blankenberg
7f89a78f35
Add tool for profiling locally cached annotations from the UCSC table browser.
2008-04-09 17:34:35 +00:00
Wen-Yu Chung
b8265695d2
add a new tool (poisson2test) with funcitonal test data to taxonomy section.
2008-04-08 15:05:43 +00:00
Wen-Yu Chung
67986d25f6
sorry, hit the wrong button (want to click cancel but click ok instead).
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add two tools and functional test data for short reads.
update tool_conf.xml.sample.
2008-03-31 19:29:00 +00:00
Wen-Yu Chung
163e4bc200
2008-03-31 19:24:56 +00:00
Wen-Yu Chung
598462643a
update ucsc builds.txt. now blat tool should pass functional test.
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also update boxplot config file.
2008-03-28 16:07:00 +00:00
Wen-Yu Chung
9adee0844d
update short reads tools. add functional test data.
2008-03-27 22:11:18 +00:00
Daniel Blankenberg
3025531e0b
Add a tool that allows species based concatenation of FASTA files. Useful for manipulating the results of MAF to FASTA conversion or stitching.
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This does not work on the results of the Extract Genomic DNA tool, since it uses a different header style.
2008-03-27 17:58:47 +00:00
Anton Nekrutenko
41769817da
more tax fixes
2008-03-21 15:15:11 +00:00
Anton Nekrutenko
2d14d029ea
Added taxonomy to tool_comf.xml.sample
2008-03-20 19:54:32 +00:00
Guruprasad Anada
89bb493d3c
Adding new tool to estimate insertion and deletion rates from 3-way alignments.
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Also, modified 'Fetch Indels' tool.
2008-03-13 16:21:39 +00:00
Guruprasad Anada
b032b71bc0
Adding tool to fetch closest upstream and downstream features for a given set of intervals.
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Added: Tool xml and py files, test data.
Modified: tool_conf.xml.sample.
2008-03-05 20:08:01 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
4dd1f044e1
Removed tool version directiories for some of the tools...the rest soon.
2008-03-03 16:14:06 +00:00
Greg Von Kuster
335ebef0af
Restored version 1.1.0 of aggregate scores tool and moved the fixes to version 1.1.1.
2008-02-28 00:08:05 +00:00
Wen-Yu Chung
5b4e5a772b
modify data structure used in short read tools.
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update functional test data.
2008-02-25 18:42:39 +00:00
Anton Nekrutenko
f607e77b6a
Tool for changing case
2008-02-25 15:15:18 +00:00
Greg Von Kuster
9262212acd
Added tool version directories for validation and visualization tools directories.
2008-02-22 20:36:20 +00:00
Greg Von Kuster
78b2d4b78e
Added tool version directories for stats tools directory.
2008-02-22 20:26:57 +00:00
Greg Von Kuster
b75509fa17
Added tool version directories to regVariation tools directory.
2008-02-22 20:09:25 +00:00
Greg Von Kuster
218684f610
Added tool version directories for plotting tools directory.
2008-02-22 19:41:52 +00:00
Greg Von Kuster
99bc8db3fd
Added tool version directories to new_operations tools directory.
2008-02-22 19:23:18 +00:00
Greg Von Kuster
c2f5849504
Added tool version directories for metag_tools directory.
2008-02-22 18:44:05 +00:00
Greg Von Kuster
a2f475b55a
Added tool version directories for maf tool directory.
2008-02-22 18:35:01 +00:00
Greg Von Kuster
073d392616
Added tool version directories for hyphy tools, also added galaxy/tools/util directory to house utility code used acroos multiple tools.
2008-02-22 16:50:12 +00:00
Greg Von Kuster
b8599b819f
Finished adding tool version directories to filters tool directory.
2008-02-22 15:48:05 +00:00
Greg Von Kuster
32b40a5f27
Added more tool version directories for filters tool directoy.
2008-02-22 15:23:46 +00:00
Greg Von Kuster
37eeb64f61
Added tool version directory hierarchy for some tools in the filters tool directory.
2008-02-22 14:57:00 +00:00
Guruprasad Anada