Kelly Vincent
f2aaa29988
Updated Bowtie wrapper tool to add a number of threads parameter and remove two unnecessary options
2009-09-14 14:54:11 -04:00
Kelly Vincent
e13eaf8a0c
Added Bowtie wrapper tool
2009-09-11 14:38:05 -04:00
Guruprasad Anada
140b458dbb
Bug fix for 'Fetch closest feature' tool.
2009-09-10 17:35:21 -04:00
Nate Coraor
6f3a169b01
Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally
2009-09-10 14:52:38 -04:00
Daniel Blankenberg
c8ddfaaadb
Fix heading for Example 2 in maf_split_by_species onscreen tool help.
2009-09-04 11:08:10 -04:00
Daniel Blankenberg
6de4ac1c27
removing debuging statements from annotation_profiler that were never inteded to go out
2009-09-04 10:49:02 -04:00
Daniel Blankenberg
87eebd3206
First pass at allowing MAF tools to deal with multiple occurrences of a species within a block. Tool versions have been incremented as necessary.
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These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index.
A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once.
2009-09-04 10:40:16 -04:00
Anton Nekrutenko
61c7d63087
Added pileup parser. Pardon the perl = used to its regexes too much
2009-09-04 10:23:37 -04:00
Guruprasad Anada
13ef14c6dd
Added a new option to 'fetch closest features' tool to return the closest feature either upstream or downstream.
2009-09-02 13:36:16 -04:00
Kelly Vincent
1008d8692f
Added several options to the Samtools pileup tool
2009-09-01 17:01:44 -04:00
Kelly Vincent
9d0dd5f7ce
Added samtools-based tools (sam_to_bam, sam_merge, sam_pileup) with their supporting files and modified Bam datatype so temp files are properly cleaned up
2009-08-28 15:59:16 -04:00
Nate Coraor
2e407c0b21
Fix for multi-byte file uploads
2009-08-25 14:58:37 -04:00
Nate Coraor
4158ee0833
set job state to new in upload tool action so that track_jobs_in_database works
2009-08-25 11:53:42 -04:00
Guruprasad Anada
d72d1a7205
Change dbkey of unmapped liftover dataset to the input dataset's dbkey.
2009-08-21 11:40:51 -04:00
Anton Nekrutenko
bf9666bf21
Fixed a stupid and truly horrible paired end splitter bug
2009-08-20 17:33:39 -04:00
Nate Coraor
3f5da01132
Real Job(tm) upload support
2009-08-20 10:49:54 -04:00
James Taylor
95100849be
Merge.
2009-08-19 17:51:46 -04:00
Kanwei Li
e63bd72334
Typo
2009-08-19 11:33:58 -04:00
Greg Von Kuster
d0d7875192
Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.
2009-08-14 15:37:31 -04:00
Daniel Blankenberg
b1fbae947b
Testing framework will now click the add button for nested repeats when repeat content has been specfied.
2009-08-05 11:54:34 -04:00
Daniel Blankenberg
0e651adbe1
Allow nested groupings in testing framework.
2009-08-05 08:58:23 -04:00
Kelly Vincent
f5d67cda72
Renamed test files and fixed output datatype problem with solid-to-fastq tool
2009-08-04 16:32:57 -04:00
Kelly Vincent
57f0f10d38
Commented out failing test in solid_to_fastq and added test files that fastq_conversions relies on
2009-08-03 16:58:22 -04:00
Guruprasad Anada
bcd0192709
Fix bar chart output format.
2009-08-03 16:38:27 -04:00
Daniel Blankenberg
da67dccfda
Fix megablast wrapper never cleaning up tempfiles.
2009-08-03 16:23:37 -04:00
Daniel Blankenberg
b2e2b801ea
Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is
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greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user.
Tools using this script have been updated to provide the max file size on the command line.
Resolves ticket #93 .
2009-08-03 12:02:54 -04:00
Kelly Vincent
5d4b1151d0
Added solid_to_fastq and fastq_conversions converters to Convert Formats section
2009-07-31 11:48:37 -04:00
Kelly Vincent
3bbac86312
Added fastqsanger data format and required bwa_wrapper to take only that format as input
2009-07-30 12:06:24 -04:00
Kelly Vincent
5d43709a76
Removed option to select indexing algorithm from BWA wrapper and have it automatically determine the algorithm by file size.
2009-07-24 17:06:12 -04:00
Kelly Vincent
b6ea9ed1eb
Added BWA wrapper tool to Short Read Mapping Tools
2009-07-24 15:13:11 -04:00
Kelly Vincent
03f245fe15
Fixed for functional tests for new version of fasta_filter_by_length tool contributed by James Casbon.
2009-07-23 14:31:11 -04:00
Kelly Vincent
ed970b406f
Performance improvements for fasta_filter_by_length and fasta_to_tabular
2009-07-23 12:16:44 -04:00
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.
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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.
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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
Kelly Vincent