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Merge branch 'django1.4' of mus.cacr.caltech.edu:htsworkflow into django1.4
2012-08-28
Diane Trout
Attempt to come up with regexp to detect hiseq formatted...
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2012-08-09
Diane Trout
Fix some mismatches between variable names in python...
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2012-08-07
Diane Trout
Create a lane to file name turtle data file
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2012-08-07
Diane Trout
Simplify code to see if we already have a DataRun created.
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2012-08-06
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-08-06
Diane Trout
Don't link to lane for the raw result files section.
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2012-08-06
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-08-06
Diane Trout
Use default printer settings again.
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2012-08-06
Diane Trout
Test proper setting of sequence project variable
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2012-08-02
Diane Trout
Test more of the sequences class.
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2012-08-02
Diane Trout
Fix a few more formatting issues with the geo template
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2012-08-01
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-08-01
Diane Trout
GEO wanted both files for a paired lane to be on a...
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2012-07-27
Diane Trout
Fix issues introduced when switching to the django...
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2012-07-25
Diane Trout
Actually we want to capture the unanalyzed lanes if...
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2012-07-24
Diane Trout
Get actual list of sequencers used for a library.
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2012-07-23
Diane Trout
Update to our current IPs. I'm tired of syncdb overwriting...
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2012-07-19
Diane Trout
Adapt building qseq or srf archives to use SampleKey...
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2012-07-19
Diane Trout
Update save_raw_data to SampleKey api
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2012-07-19
Diane Trout
Add in a few more genomes to detection code
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2012-07-17
Diane Trout
Fix library viewing code to read HiSeq run xmls.
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2012-07-16
Diane Trout
Remove default sequence-format so the new auto-detector...
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2012-07-14
Diane Trout
Attempt to guess raw sequence type for a run.
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2012-07-13
Diane Trout
Fix a refactoring error
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2012-07-12
Diane Trout
Look for RTAConfig.xml file generated by pipeline 1...
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2012-07-12
Diane Trout
Use lane 1s matrix when pipeline was set to build matrix...
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2012-07-12
Diane Trout
Clean up flowcell ID detection and add support for...
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2012-07-12
Diane Trout
fix a variable name typo
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2012-07-12
Diane Trout
Re-enable some suppressed tests and update them for...
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2012-07-12
Diane Trout
whitespace fix.
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2012-07-11
Diane Trout
Test reading the xml out of a file too.
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2012-07-10
Diane Trout
Fix import statement and typos for genomemap
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2012-07-10
Diane Trout
Create a class to convert contig names into genome...
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2012-07-10
Diane Trout
Guess genome name for building compressed mapping counts...
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2012-07-10
Diane Trout
Give some failover defaults to printer settings.
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2012-07-07
Diane Trout
Use sample keys when looking up lane parameters.
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2012-07-06
Diane Trout
A few python 2.6 test case incompatibilities.
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2012-07-06
Diane Trout
Switch to regular dictionary instead of ordered dictionary.
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2012-07-05
Diane Trout
Massively rework eland file finding and indexing.
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2012-07-05
Diane Trout
Rename chromosome in hiseq test set to match our fake...
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2012-06-30
Diane Trout
Disable debug messages for each scanned eland file...
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2012-06-30
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-06-30
Diane Trout
Support multiple having an eland file split into multiple...
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2012-06-30
Diane Trout
Some minor tweaks to rta 1.12 testing.
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2012-06-30
Diane Trout
Properly code in tabs for simulated hiseq export files
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2012-06-30
Diane Trout
Use different tags indicating gerald or casava style...
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2012-06-27
Diane Trout
Add script for updating database to data run versions...
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2012-06-27
Diane Trout
If I'm going to make a call to logger, I really should...
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2012-06-27
Diane Trout
Only allow one default cluster station or sequencer...
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2012-06-27
Diane Trout
Only allow one default cluster station or sequencer...
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2012-06-27
Diane Trout
Auto-generate a secret key for django and store in...
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2012-06-26
Diane Trout
Add the ability to specify default cluster station...
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2012-06-26
Diane Trout
reformatting to be more pep8 like
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2012-06-25
Diane Trout
Convert dictionary comprehension to dict(generator...
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2012-06-25
Diane Trout
Adapt select strike-out widget to django 1.2
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2012-06-23
Diane Trout
Forgot to add the css file to add 'active' state to...
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2012-06-23
Diane Trout
Add an 'active' state to the sequencers.
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2012-06-22
Diane Trout
Show software version information on datarun page
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2012-06-22
Diane Trout
Save pipeline version information from run_xml into...
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2012-06-22
Diane Trout
Add links to libraries and submission to data loaded...
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2012-06-21
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htsworkflow
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2012-06-15
Diane Trout
Move typeof. I think its now getting parsed by rapper...
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2012-06-14
Diane Trout
Import information from NCBI SRA into a RDF model.
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2012-06-14
Diane Trout
Slightly different sort order for finding libraries
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2012-06-12
Diane Trout
Add a software (name) property to firecrest, ipar,...
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2012-06-11
Diane Trout
Return a gerald version number as a number and not...
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2012-06-07
Diane Trout
Add instrument ID and model to sequencer table
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2012-06-02
Diane Trout
Split lane parameters into seperate classes for GA...
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2012-05-31
Diane Trout
Fixup docstring to be clearer to others
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2012-05-25
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htsworkflow
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2012-05-25
Diane Trout
replace tab charcter with spaces in the multiplex index...
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2012-05-25
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htsworkflow
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2012-05-25
Diane Trout
Fix Multiplex index pluralization
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2012-05-23
Diane Trout
Generate html reports when doing sparql queries with...
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2012-05-16
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-05-16
Diane Trout
Tweak some test code to work with librdf 1.0.10
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2012-05-16
Diane Trout
update summary.py to extract data from HiSeq runs.
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2012-05-15
Diane Trout
Fix bugs introduduced by the improved HiSeq runfolder...
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2012-05-12
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-05-12
Diane Trout
I found this version more useful for trying to
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2012-05-12
Diane Trout
Properly constructing the geo soft file really needed...
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2012-05-12
Diane Trout
Prepare for submitting data to geo by:
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2012-05-10
Diane Trout
Minimal changes needed to get raw data archived for...
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2012-05-04
Diane Trout
100% test coverage for alphanum.py
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2012-05-03
Diane Trout
Rename a cell-line since we're now using "treatment...
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2012-04-17
Diane Trout
Add ability to override location to tar and lftp commands
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2012-04-17
Diane Trout
Rename global logger to LOGGER to be more PEP8 like
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2012-04-16
Diane Trout
Fix a typo and a missing .items() from the change of...
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2012-04-13
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-04-12
Diane Trout
Extend the adapter id field to support the dual indexed...
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2012-04-11
Diane Trout
Start developing GEO SOFT submission tool.
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2012-04-11
Diane Trout
Move code out of ucsc_gather and into the htsworkflow...
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2012-04-02
Diane Trout
Remove a dead form
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2012-03-29
Diane Trout
Change to using django templates for generating condor...
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2012-03-29
Diane Trout
Improve a settings error message, as it was confusing...
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2012-03-27
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2012-03-27
Diane Trout
Add an option to make a mini archive containing just...
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2012-03-26
Diane Trout
Switch to lxml for parsing the summary file.
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2012-03-26
Diane Trout
Remove a function from the inifile version of ucsc_gather
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2012-03-23
Diane Trout
Apparently I forgot to remove a parameter why creating...
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