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2012-08-02	Diane Trout	Fix a few more formatting issues with the geo template	commit \| commitdiff \| tree
2012-08-01	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2012-08-01	Diane Trout	GEO wanted both files for a paired lane to be on a...	commit \| commitdiff \| tree
2012-07-27	Diane Trout	Fix issues introduced when switching to the django...	commit \| commitdiff \| tree
2012-07-25	Diane Trout	Actually we want to capture the unanalyzed lanes if...	commit \| commitdiff \| tree
2012-07-24	Diane Trout	Get actual list of sequencers used for a library.	commit \| commitdiff \| tree
2012-07-23	Diane Trout	Update to our current IPs. I'm tired of syncdb overwriting...	commit \| commitdiff \| tree
2012-07-19	Diane Trout	Adapt building qseq or srf archives to use SampleKey...	commit \| commitdiff \| tree
2012-07-19	Diane Trout	Update save_raw_data to SampleKey api	commit \| commitdiff \| tree
2012-07-19	Diane Trout	Add in a few more genomes to detection code	commit \| commitdiff \| tree
2012-07-17	Diane Trout	Fix library viewing code to read HiSeq run xmls.	commit \| commitdiff \| tree
2012-07-16	Diane Trout	Remove default sequence-format so the new auto-detector...	commit \| commitdiff \| tree
2012-07-14	Diane Trout	Attempt to guess raw sequence type for a run.	commit \| commitdiff \| tree
2012-07-13	Diane Trout	Fix a refactoring error	commit \| commitdiff \| tree
2012-07-12	Diane Trout	Look for RTAConfig.xml file generated by pipeline 1...	commit \| commitdiff \| tree
2012-07-12	Diane Trout	Use lane 1s matrix when pipeline was set to build matrix...	commit \| commitdiff \| tree
2012-07-12	Diane Trout	Clean up flowcell ID detection and add support for...	commit \| commitdiff \| tree
2012-07-12	Diane Trout	fix a variable name typo	commit \| commitdiff \| tree
2012-07-12	Diane Trout	Re-enable some suppressed tests and update them for...	commit \| commitdiff \| tree
2012-07-12	Diane Trout	whitespace fix.	commit \| commitdiff \| tree
2012-07-11	Diane Trout	Test reading the xml out of a file too.	commit \| commitdiff \| tree
2012-07-10	Diane Trout	Fix import statement and typos for genomemap	commit \| commitdiff \| tree
2012-07-10	Diane Trout	Create a class to convert contig names into genome...	commit \| commitdiff \| tree
2012-07-10	Diane Trout	Guess genome name for building compressed mapping counts...	commit \| commitdiff \| tree
2012-07-10	Diane Trout	Give some failover defaults to printer settings.	commit \| commitdiff \| tree
2012-07-07	Diane Trout	Use sample keys when looking up lane parameters.	commit \| commitdiff \| tree
2012-07-06	Diane Trout	A few python 2.6 test case incompatibilities.	commit \| commitdiff \| tree
2012-07-06	Diane Trout	Switch to regular dictionary instead of ordered dictionary.	commit \| commitdiff \| tree
2012-07-05	Diane Trout	Massively rework eland file finding and indexing.	commit \| commitdiff \| tree
2012-07-05	Diane Trout	Rename chromosome in hiseq test set to match our fake...	commit \| commitdiff \| tree
2012-06-30	Diane Trout	Disable debug messages for each scanned eland file...	commit \| commitdiff \| tree
2012-06-30	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2012-06-30	Diane Trout	Support multiple having an eland file split into multiple...	commit \| commitdiff \| tree
2012-06-30	Diane Trout	Some minor tweaks to rta 1.12 testing.	commit \| commitdiff \| tree
2012-06-30	Diane Trout	Properly code in tabs for simulated hiseq export files	commit \| commitdiff \| tree
2012-06-30	Diane Trout	Use different tags indicating gerald or casava style...	commit \| commitdiff \| tree
2012-06-27	Diane Trout	Add script for updating database to data run versions...	commit \| commitdiff \| tree
2012-06-27	Diane Trout	If I'm going to make a call to logger, I really should...	commit \| commitdiff \| tree
2012-06-27	Diane Trout	Only allow one default cluster station or sequencer...	commit \| commitdiff \| tree
2012-06-27	Diane Trout	Only allow one default cluster station or sequencer...	commit \| commitdiff \| tree
2012-06-27	Diane Trout	Auto-generate a secret key for django and store in...	commit \| commitdiff \| tree
2012-06-26	Diane Trout	Add the ability to specify default cluster station...	commit \| commitdiff \| tree
2012-06-26	Diane Trout	reformatting to be more pep8 like	commit \| commitdiff \| tree
2012-06-25	Diane Trout	Convert dictionary comprehension to dict(generator...	commit \| commitdiff \| tree
2012-06-25	Diane Trout	Adapt select strike-out widget to django 1.2	commit \| commitdiff \| tree
2012-06-23	Diane Trout	Forgot to add the css file to add 'active' state to...	commit \| commitdiff \| tree
2012-06-23	Diane Trout	Add an 'active' state to the sequencers.	commit \| commitdiff \| tree
2012-06-22	Diane Trout	Show software version information on datarun page	commit \| commitdiff \| tree
2012-06-22	Diane Trout	Save pipeline version information from run_xml into...	commit \| commitdiff \| tree
2012-06-22	Diane Trout	Add links to libraries and submission to data loaded...	commit \| commitdiff \| tree
2012-06-21	Diane Trout	Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htsworkflow	commit \| commitdiff \| tree
2012-06-15	Diane Trout	Move typeof. I think its now getting parsed by rapper...	commit \| commitdiff \| tree
2012-06-14	Diane Trout	Import information from NCBI SRA into a RDF model.	commit \| commitdiff \| tree
2012-06-14	Diane Trout	Slightly different sort order for finding libraries	commit \| commitdiff \| tree
2012-06-12	Diane Trout	Add a software (name) property to firecrest, ipar,...	commit \| commitdiff \| tree
2012-06-11	Diane Trout	Return a gerald version number as a number and not...	commit \| commitdiff \| tree
2012-06-07	Diane Trout	Add instrument ID and model to sequencer table	commit \| commitdiff \| tree
2012-06-02	Diane Trout	Split lane parameters into seperate classes for GA...	commit \| commitdiff \| tree
2012-05-31	Diane Trout	Fixup docstring to be clearer to others	commit \| commitdiff \| tree
2012-05-25	Diane Trout	Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htsworkflow	commit \| commitdiff \| tree
2012-05-25	Diane Trout	replace tab charcter with spaces in the multiplex index...	commit \| commitdiff \| tree
2012-05-25	Diane Trout	Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htsworkflow	commit \| commitdiff \| tree
2012-05-25	Diane Trout	Fix Multiplex index pluralization	commit \| commitdiff \| tree
2012-05-23	Diane Trout	Generate html reports when doing sparql queries with...	commit \| commitdiff \| tree
2012-05-16	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2012-05-16	Diane Trout	Tweak some test code to work with librdf 1.0.10	commit \| commitdiff \| tree
2012-05-16	Diane Trout	update summary.py to extract data from HiSeq runs.	commit \| commitdiff \| tree
2012-05-15	Diane Trout	Fix bugs introduduced by the improved HiSeq runfolder...	commit \| commitdiff \| tree
2012-05-12	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2012-05-12	Diane Trout	I found this version more useful for trying to	commit \| commitdiff \| tree
2012-05-12	Diane Trout	Properly constructing the geo soft file really needed...	commit \| commitdiff \| tree
2012-05-12	Diane Trout	Prepare for submitting data to geo by:	commit \| commitdiff \| tree
2012-05-10	Diane Trout	Minimal changes needed to get raw data archived for...	commit \| commitdiff \| tree
2012-05-04	Diane Trout	100% test coverage for alphanum.py	commit \| commitdiff \| tree
2012-05-03	Diane Trout	Rename a cell-line since we're now using "treatment...	commit \| commitdiff \| tree
2012-04-17	Diane Trout	Add ability to override location to tar and lftp commands	commit \| commitdiff \| tree
2012-04-17	Diane Trout	Rename global logger to LOGGER to be more PEP8 like	commit \| commitdiff \| tree
2012-04-16	Diane Trout	Fix a typo and a missing .items() from the change of...	commit \| commitdiff \| tree
2012-04-13	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2012-04-12	Diane Trout	Extend the adapter id field to support the dual indexed...	commit \| commitdiff \| tree
2012-04-11	Diane Trout	Start developing GEO SOFT submission tool.	commit \| commitdiff \| tree
2012-04-11	Diane Trout	Move code out of ucsc_gather and into the htsworkflow...	commit \| commitdiff \| tree
2012-04-02	Diane Trout	Remove a dead form	commit \| commitdiff \| tree
2012-03-29	Diane Trout	Change to using django templates for generating condor...	commit \| commitdiff \| tree
2012-03-29	Diane Trout	Improve a settings error message, as it was confusing...	commit \| commitdiff \| tree
2012-03-27	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2012-03-27	Diane Trout	Add an option to make a mini archive containing just...	commit \| commitdiff \| tree
2012-03-26	Diane Trout	Switch to lxml for parsing the summary file.	commit \| commitdiff \| tree
2012-03-26	Diane Trout	Remove a function from the inifile version of ucsc_gather	commit \| commitdiff \| tree
2012-03-23	Diane Trout	Apparently I forgot to remove a parameter why creating...	commit \| commitdiff \| tree
2012-03-23	Diane Trout	Add fastq to the raw format add_xoption	commit \| commitdiff \| tree
2012-03-23	Diane Trout	Add a rdf type for ucsc track records	commit \| commitdiff \| tree
2012-03-22	Diane Trout	Messed up the RDFa for specifying that a library was...	commit \| commitdiff \| tree
2012-03-22	Diane Trout	Use name instead of library_name as the property describing...	commit \| commitdiff \| tree
2012-03-08	Diane Trout	Actually if I provide an output file, I want to write...	commit \| commitdiff \| tree
2012-03-08	Diane Trout	Change name of term used for conditions to condition_term	commit \| commitdiff \| tree
2012-03-07	Diane Trout	Update archive script to try and deal with HiSeq multiplexed...	commit \| commitdiff \| tree
2012-03-07	Diane Trout	Always include the python path when generating the...	commit \| commitdiff \| tree
2012-03-07	Diane Trout	Forgot to add split attribute to __eq__ test.	commit \| commitdiff \| tree
2012-03-07	Diane Trout	Add extract HiSeq project based split fastq files to...	commit \| commitdiff \| tree
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