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2009-01-08	Diane Trout	This is a partial merge of the stanford branch with...	commit \| commitdiff \| tree
2009-01-06	Diane Trout	Look in Temp directories for some of the files we have...	commit \| commitdiff \| tree
2008-12-24	Diane Trout	Handle paired-end eland files.	commit \| commitdiff \| tree
2008-12-24	Diane Trout	remove a debug print statement	commit \| commitdiff \| tree
2008-12-24	Diane Trout	Add test cases for alphanum sort	commit \| commitdiff \| tree
2008-12-24	Diane Trout	Support sorting numbers along with the alphanumeric...	commit \| commitdiff \| tree
2008-12-23	Diane Trout	change from hand coded formatting functions to the...	commit \| commitdiff \| tree
2008-12-23	Diane Trout	Use the right URLError attribute names for error messages	commit \| commitdiff \| tree
2008-12-22	Diane Trout	update make-tree-library script with new default location	commit \| commitdiff \| tree
2008-12-22	Diane Trout	fix the multi-eland parser to strip off extensions...	commit \| commitdiff \| tree
2008-12-22	Diane Trout	clean up the logic for deciding the output filename...	commit \| commitdiff \| tree
2008-12-19	Diane Trout	Add command to report path to make figuring out which...	commit \| commitdiff \| tree
2008-12-18	Diane Trout	rename config file to something that doesn't include...	commit \| commitdiff \| tree
2008-12-10	Diane Trout	The summary parsing code now seems to handle paired...	commit \| commitdiff \| tree
2008-12-09	Diane Trout	Test 1.1rc1 style runs, which unfortunately require...	commit \| commitdiff \| tree
2008-12-03	Diane Trout	make-library-tree is a tool to maintain caltech's version...	commit \| commitdiff \| tree
2008-12-03	Diane Trout	Add test code to see if runfolder can handle something...	commit \| commitdiff \| tree
2008-12-03	Diane Trout	Add code to create a paired end Summary.htm file	commit \| commitdiff \| tree
2008-12-03	Diane Trout	Store the bustard pathname when searching for run folders	commit \| commitdiff \| tree
2008-11-21	Diane Trout	Use the get_runs from htsworkflow.pipelines.runfolder	commit \| commitdiff \| tree
2008-11-14	Diane Trout	Forgot to change a import htsworkflow.pipeline to htsworflow...	commit \| commitdiff \| tree
2008-11-06	Diane Trout	Updated ipar_100 test case to deal with the using U0...	commit \| commitdiff \| tree
2008-11-06	Diane Trout	Process eland extended (or multi) read files.	commit \| commitdiff \| tree
2008-10-30	Diane Trout	The htsworkflow.pipelines.gerald module was getting...	commit \| commitdiff \| tree
2008-10-30	Diane Trout	Add support for scanning for results in the IPAR directory.	commit \| commitdiff \| tree
2008-10-30	Diane Trout	Add "_slow" to the end of the queuecommand test functions	commit \| commitdiff \| tree
2008-10-28	Diane Trout	update setup.py for some package renames and some missing...	commit \| commitdiff \| tree
2008-10-21	Diane Trout	Merge in new modules from htsworkflow branch.	commit \| commitdiff \| tree
2008-10-21	Diane Trout	Merge in model changes to fctracker from htsworkflow...	commit \| commitdiff \| tree
2008-10-21	Diane Trout	update scripts for the pipeline to pipelines module...	commit \| commitdiff \| tree
2008-10-15	Diane Trout	rename pipeline to pipelines to imply that we can process...	commit \| commitdiff \| tree
2008-10-15	Diane Trout	Rename trunk from gaworkflow to htsworkflow (and update...	commit \| commitdiff \| tree
2008-09-25	Diane Trout	solexa2srf likes to produce output, so my trick of...	commit \| commitdiff \| tree
2008-09-25	Diane Trout	use _ for field seperator in srf file names. (Using...	commit \| commitdiff \| tree
2008-09-18	Diane Trout	Use queuecommands.run not queuecommands.start_job to...	commit \| commitdiff \| tree
2008-09-18	Diane Trout	Be a little more informative about how many process...	commit \| commitdiff \| tree
2008-09-05	Diane Trout	extract status field out of flowcell name.	commit \| commitdiff \| tree
2008-08-29	Diane Trout	Add support for converting mutli-eland files from pipeline...	commit \| commitdiff \| tree
2008-08-29	Diane Trout	insert stub clean_runs function to list roughly what...	commit \| commitdiff \| tree
2008-08-15	Diane Trout	Improve code to extract runfolder name from the path...	commit \| commitdiff \| tree
2008-08-14	Diane Trout	In trying to get scripts/srf to work I needed to set...	commit \| commitdiff \| tree
2008-08-14	Diane Trout	refactor code to make a runfolder out of the UnitTest...	commit \| commitdiff \| tree
2008-08-14	Diane Trout	we might as well automatically save the Summary.htm...	commit \| commitdiff \| tree
2008-08-14	Diane Trout	Utility to create srf files from a bustard directory	commit \| commitdiff \| tree
2008-08-11	Diane Trout	A bit of refactoring toward making the run progress...	commit \| commitdiff \| tree
2008-07-16	Diane Trout	The older pipeline runs had a Phi-X control lane which...	commit \| commitdiff \| tree
2008-07-15	Diane Trout	Provide cross referencing information to the libraries...	commit \| commitdiff \| tree
2008-07-07	Diane Trout	Finish updating the Summary parsing file to handle...	commit \| commitdiff \| tree
2008-07-03	Diane Trout	Partially handle the changed Summary.htm file from...	commit \| commitdiff \| tree
2008-06-24	Diane Trout	Detect if our watch is on a mount point.	commit \| commitdiff \| tree
2008-06-17	Diane Trout	Add QueueCommands, a class that allows controlling...	commit \| commitdiff \| tree
2008-06-06	Diane Trout	don't use os.path.normpath when pathname is null in...	commit \| commitdiff \| tree
2008-06-05	Diane Trout	add --extract-results to scripts/runfolder	commit \| commitdiff \| tree
2008-05-29	Diane Trout	Some of the older flow cells used a default genome...	commit \| commitdiff \| tree
2008-05-28	Diane Trout	Compute all the details needed to create our 25bp rerun...	commit \| commitdiff \| tree
2008-05-27	Diane Trout	ignore more *.py[co~] files in some of our test directories	commit \| commitdiff \| tree
2008-05-23	Diane Trout	add --run-xml to runfolder so you can generate summary...	commit \| commitdiff \| tree
2008-05-23	Diane Trout	Update pipeline.gerald to handle eland_result files...	commit \| commitdiff \| tree
2008-05-15	Diane Trout	add rerun_eland.py which extracts sub-sequences from...	commit \| commitdiff \| tree
2008-05-14	Diane Trout	separate computing the sample/lane_id names from calculating...	commit \| commitdiff \| tree
2008-05-13	Diane Trout	add additional debugging logging to retrieve_config...	commit \| commitdiff \| tree
2008-05-13	Diane Trout	logging.basicConfig should only be in top level scripts.	commit \| commitdiff \| tree
2008-05-10	Diane Trout	make it possible to include all alignments, not just...	commit \| commitdiff \| tree
2008-05-10	Diane Trout	makebed is a script too	commit \| commitdiff \| tree
2008-05-10	Diane Trout	Keep track of sample_name and lane_id computed from...	commit \| commitdiff \| tree
2008-05-09	Diane Trout	Make the runfolder splitting patch a bit more python...	commit \| commitdiff \| tree
2008-05-09	Diane Trout	update the setup.py file to the new name for the runfolder...	commit \| commitdiff \| tree
2008-05-09	Diane Trout	Move runfolder analysis classes out of scripts/runfolder...	commit \| commitdiff \| tree
2008-04-24	Diane Trout	Add a script that takes a set of eland_result files...	commit \| commitdiff \| tree
2008-04-24	Diane Trout	Report cluster results with the rest of the lane summary...	commit \| commitdiff \| tree
2008-04-22	Diane Trout	also since nothing is currently using the pipelineFinished...	commit \| commitdiff \| tree
2008-04-22	Diane Trout	oops forgot to remove some debugging statements from...	commit \| commitdiff \| tree
2008-04-22	Diane Trout	Extend makebed to lookup metadata out of a copy of...	commit \| commitdiff \| tree
2008-04-21	Diane Trout	split the library script into a reusable database/reporting...	commit \| commitdiff \| tree
2008-04-21	Diane Trout	Ignore binary files generated by python (*.py[co])	commit \| commitdiff \| tree
2008-04-09	Diane Trout	Add library.py, a script to extract a useful description...	commit \| commitdiff \| tree
2008-04-01	Diane Trout	Don't die if Config/FlowcellId.xml is missing warn...	commit \| commitdiff \| tree
2008-04-01	Diane Trout	report statistics on the various eland_result sequence...	commit \| commitdiff \| tree
2008-03-28	Diane Trout	Don't die if Summary.htm isn't present	commit \| commitdiff \| tree
2008-03-28	Diane Trout	rename the summary report to summary_report to distingush...	commit \| commitdiff \| tree
2008-03-28	Diane Trout	make the mapped reads summary report more robust	commit \| commitdiff \| tree
2008-03-27	Diane Trout	Add runfolder.py to the list of scripts	commit \| commitdiff \| tree
2008-03-26	Diane Trout	sort the sample mapped reads output	commit \| commitdiff \| tree
2008-03-25	Diane Trout	Add documentation about what runfolder.py does	commit \| commitdiff \| tree
2008-03-22	Diane Trout	Store the firecrest/bustard/gerald tuple in a new class...	commit \| commitdiff \| tree
2008-03-21	Diane Trout	Summarize information from the runfolder.	commit \| commitdiff \| tree
2008-03-06	Diane Trout	convert a single-match eland result file into a bed...	commit \| commitdiff \| tree
2008-03-06	Diane Trout	Add script to extract some subset of sequence from...	commit \| commitdiff \| tree
2008-01-29	Diane Trout	DummyOptions didn't define a genome_dir member before...	commit \| commitdiff \| tree
2008-01-23	Diane Trout	return most recent genome build for the pipeline config...	commit \| commitdiff \| tree
2008-01-15	Diane Trout	Oops, forgot to provide a null body to my the stub...	commit \| commitdiff \| tree
2008-01-15	Diane Trout	pyinotify rm_watch takes a list, not a dictionary.	commit \| commitdiff \| tree
2008-01-15	Diane Trout	Update test_copier to reflect copiers move to gaworkflow...	commit \| commitdiff \| tree
2008-01-15	Diane Trout	move the autotmation scripts into gaworkflow.automation	commit \| commitdiff \| tree
2008-01-11	Diane Trout	Add the xmi file from umbrello documenting our basic...	commit \| commitdiff \| tree
2008-01-09	Diane Trout	always trigger a copy when we receive the sequencingFinshed...	commit \| commitdiff \| tree
2008-01-08	Diane Trout	tell subversion to ignore *.py[co~] files	commit \| commitdiff \| tree
2008-01-08	Diane Trout	make sequencingFinished return something instead of...	commit \| commitdiff \| tree
2008-01-08	Diane Trout	Remove unnecessary code from the runner.py module	commit \| commitdiff \| tree
2008-01-08	Diane Trout	Add script to make it easier to launch runner	commit \| commitdiff \| tree
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htsworkflow sequencing LIMS software

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