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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
2012-04-12	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
2012-03-08	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
2012-03-07	Diane Trout	Update help message since we have a new type of file...	commit \| commitdiff \| tree
2012-03-06	Diane Trout	Support scanning for split fastq files generated by...	commit \| commitdiff \| tree
2012-03-06	Diane Trout	Ignore some more coverage files	commit \| commitdiff \| tree
2012-03-06	Diane Trout	Add module to convert multiple fastq files into a single...	commit \| commitdiff \| tree
2012-03-06	Diane Trout	Add ability to print out json structures returned by...	commit \| commitdiff \| tree
2012-03-05	Diane Trout	Use named tuple for sequence flowcell/start/stop/project...	commit \| commitdiff \| tree
2012-03-02	Diane Trout	Core functions for saving and finding fastq files generated...	commit \| commitdiff \| tree
2012-03-01	Diane Trout	Remove some debug prints	commit \| commitdiff \| tree
2012-03-01	Diane Trout	Simulate a HiSeq runfolder.	commit \| commitdiff \| tree
2012-02-02	Diane Trout	Make report prettier.	commit \| commitdiff \| tree
2012-01-31	Diane Trout	Shorten option for specifying model name.	commit \| commitdiff \| tree
2012-01-30	Diane Trout	Fix a typo in some RDF example data	commit \| commitdiff \| tree
2012-01-30	Diane Trout	Make it possible to filter which genome to run report...	commit \| commitdiff \| tree
2012-01-30	Diane Trout	Add ability to refresh library data from our htsw server	commit \| commitdiff \| tree
2012-01-25	Diane Trout	Start writing a report for "so, what experiments have...	commit \| commitdiff \| tree
2012-01-25	Diane Trout	Added scanning for libraries that aren't attached to...	commit \| commitdiff \| tree
2012-01-25	Diane Trout	split a function into two. (A query execute function...	commit \| commitdiff \| tree
2012-01-25	Diane Trout	Changed pprint daf attributes to a pformat output via...	commit \| commitdiff \| tree
2012-01-25	Diane Trout	Fix 'typo' in a library URN.	commit \| commitdiff \| tree
2012-01-23	Diane Trout	Don't use assertIn as older ubuntu python doesn't have it	commit \| commitdiff \| tree
2012-01-23	Diane Trout	Invalid library IDs should 404, not return a useless...	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Handle dateTime timestamps in RDF.Nodes	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2011-12-20	Diane Trout	whitespace reformatting	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Move ucsc_encode_submission code out of extra so nose...	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Remove eXecute bit from modules	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Include the test data for testing importing ucsc download...	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Add in test code for testing downloading the ucsc download...	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Deleted obsolete tests	commit \| commitdiff \| tree
2011-12-20	Diane Trout	Try to figure out where UCSC is hosting our submitted...	commit \| commitdiff \| tree
2011-11-22	Diane Trout	Add a method to override command used to convert srf...	commit \| commitdiff \| tree
2011-11-07	Diane Trout	Use Node.uri instead of manually trimming off RDF.Node...	commit \| commitdiff \| tree
2011-11-07	Diane Trout	Function generating index text was assuming there'd...	commit \| commitdiff \| tree
2011-11-07	Diane Trout	Update library adapter type initial data to match loriens...	commit \| commitdiff \| tree
2011-11-07	Diane Trout	Merge in removal of queuecommand sleep.	commit \| commitdiff \| tree
2011-11-05	Diane Trout	Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow	commit \| commitdiff \| tree
2011-11-04	Diane Trout	Use a logger initialized to the module name much more...	commit \| commitdiff \| tree
2011-11-04	Diane Trout	Lorian renamed some of the libraries, change our hard...	commit \| commitdiff \| tree
2011-10-21	Diane Trout	Yes generate regular gerald config file.	commit \| commitdiff \| tree
2011-10-18	Diane Trout	Add library adapter type to filter choices,	commit \| commitdiff \| tree
2011-10-13	Diane Trout	Allow replicates 5 & 6	commit \| commitdiff \| tree
2011-10-11	Diane Trout	Use "not run" instead of todo to describe libraries...	commit \| commitdiff \| tree
2011-10-11	Diane Trout	Add a todo view that shows only libraries that have no	commit \| commitdiff \| tree
2011-10-10	Diane Trout	Remove ReadPrep and Thumbnail_Images being generated...	commit \| commitdiff \| tree
2011-10-10	Diane Trout	Don't need to duplicate %t tile in srf command	commit \| commitdiff \| tree
2011-10-06	Diane Trout	Add the ability to specify a flowcell id instead of...	commit \| commitdiff \| tree
2011-10-04	Diane Trout	Add support for flowcells analyzed with Casava 1.7	commit \| commitdiff \| tree
2011-09-30	Diane Trout	Sparql query to back create protocol & treatment from...	commit \| commitdiff \| tree
2011-09-30	Diane Trout	find submissions, even those without a set creation...	commit \| commitdiff \| tree
2011-09-30	Diane Trout	store md5sum of daf files to group different submissions	commit \| commitdiff \| tree
2011-09-30	Diane Trout	Configure daf variables in only one place. (daf.py)	commit \| commitdiff \| tree
2011-09-30	Diane Trout	Add support for new "extraVariables" term in DAF.	commit \| commitdiff \| tree
2011-09-22	Diane Trout	Mark library & flowcell as a type in RDF.	commit \| commitdiff \| tree
2011-09-21	Diane Trout	Switch from beautifulsoup to lxml, now that I know...	commit \| commitdiff \| tree
2011-09-21	Diane Trout	Rename ucsc submission namespace to be more consistent...	commit \| commitdiff \| tree
2011-09-19	Diane Trout	Output samples that don't have index sequence as well.	commit \| commitdiff \| tree
2011-09-19	Diane Trout	Python 2.6's DictWriter doesn't have writeheader, so...	commit \| commitdiff \| tree
2011-09-17	Diane Trout	Disable csrf protection for the json urls	commit \| commitdiff \| tree
2011-09-17	Diane Trout	Add support for tracking the multiplex index sequence.	commit \| commitdiff \| tree
2011-09-12	Diane Trout	Add support for first-gen HiSeq flowcells (e.g. ABXX)	commit \| commitdiff \| tree
2011-09-08	Diane Trout	Django 1.1's csrf protection appears to be handled...	commit \| commitdiff \| tree
2011-09-08	Diane Trout	Add links to the admin page on the public pages if...	commit \| commitdiff \| tree
2011-09-08	Diane Trout	Make it so the login link redirects you back to the...	commit \| commitdiff \| tree
2011-09-08	Diane Trout	Emacs stripped off trailing whitespace	commit \| commitdiff \| tree
2011-09-07	Diane Trout	Add link to admin page to flowcell & library pages...	commit \| commitdiff \| tree
2011-09-07	Diane Trout	Remove margin-right command as it was making a giant...	commit \| commitdiff \| tree
2011-09-02	Diane Trout	Ignore some files generated by my (diane's) development...	commit \| commitdiff \| tree
2011-09-02	Diane Trout	Attempt to download DAF data for a encodesubmit submission	commit \| commitdiff \| tree
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