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Recent IPAR xml config blocks include the runfolder name
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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2012-03-23
Diane Trout
Add fastq to the raw format add_xoption
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2012-03-23
Diane Trout
Add a rdf type for ucsc track records
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2012-03-22
Diane Trout
Messed up the RDFa for specifying that a library was...
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2012-03-22
Diane Trout
Use name instead of library_name as the property describing...
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2012-03-08
Diane Trout
Actually if I provide an output file, I want to write...
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2012-03-08
Diane Trout
Change name of term used for conditions to condition_term
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2012-03-07
Diane Trout
Update archive script to try and deal with HiSeq multiplexed...
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2012-03-07
Diane Trout
Always include the python path when generating the...
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2012-03-07
Diane Trout
Forgot to add split attribute to __eq__ test.
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2012-03-07
Diane Trout
Add extract HiSeq project based split fastq files to...
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2012-03-07
Diane Trout
Update help message since we have a new type of file...
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2012-03-06
Diane Trout
Support scanning for split fastq files generated by...
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2012-03-06
Diane Trout
Ignore some more coverage files
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2012-03-06
Diane Trout
Add module to convert multiple fastq files into a single...
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2012-03-06
Diane Trout
Add ability to print out json structures returned by...
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2012-03-05
Diane Trout
Use named tuple for sequence flowcell/start/stop/project...
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2012-03-02
Diane Trout
Core functions for saving and finding fastq files generated...
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2012-03-01
Diane Trout
Remove some debug prints
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2012-03-01
Diane Trout
Simulate a HiSeq runfolder.
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2012-02-02
Diane Trout
Make report prettier.
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2012-01-31
Diane Trout
Shorten option for specifying model name.
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2012-01-30
Diane Trout
Fix a typo in some RDF example data
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2012-01-30
Diane Trout
Make it possible to filter which genome to run report...
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2012-01-30
Diane Trout
Add ability to refresh library data from our htsw server
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2012-01-25
Diane Trout
Start writing a report for "so, what experiments have...
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2012-01-25
Diane Trout
Added scanning for libraries that aren't attached to...
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2012-01-25
Diane Trout
split a function into two. (A query execute function...
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2012-01-25
Diane Trout
Changed pprint daf attributes to a pformat output via...
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2012-01-25
Diane Trout
Fix 'typo' in a library URN.
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2012-01-23
Diane Trout
Don't use assertIn as older ubuntu python doesn't have it
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2012-01-23
Diane Trout
Invalid library IDs should 404, not return a useless...
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2011-12-20
Diane Trout
Handle dateTime timestamps in RDF.Nodes
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2011-12-20
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2011-12-20
Diane Trout
whitespace reformatting
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2011-12-20
Diane Trout
Move ucsc_encode_submission code out of extra so nose...
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2011-12-20
Diane Trout
Remove eXecute bit from modules
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2011-12-20
Diane Trout
Include the test data for testing importing ucsc download...
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2011-12-20
Diane Trout
Add in test code for testing downloading the ucsc download...
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2011-12-20
Diane Trout
Deleted obsolete tests
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2011-12-20
Diane Trout
Try to figure out where UCSC is hosting our submitted...
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2011-11-22
Diane Trout
Add a method to override command used to convert srf...
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2011-11-07
Diane Trout
Use Node.uri instead of manually trimming off RDF.Node...
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2011-11-07
Diane Trout
Function generating index text was assuming there'd...
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2011-11-07
Diane Trout
Update library adapter type initial data to match loriens...
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2011-11-07
Diane Trout
Merge in removal of queuecommand sleep.
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2011-11-05
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
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2011-11-04
Diane Trout
Use a logger initialized to the module name much more...
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2011-11-04
Diane Trout
Lorian renamed some of the libraries, change our hard...
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2011-10-21
Diane Trout
Yes generate regular gerald config file.
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2011-10-18
Diane Trout
Add library adapter type to filter choices,
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2011-10-13
Diane Trout
Allow replicates 5 & 6
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2011-10-11
Diane Trout
Use "not run" instead of todo to describe libraries...
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2011-10-11
Diane Trout
Add a todo view that shows only libraries that have no
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2011-10-10
Diane Trout
Remove ReadPrep and Thumbnail_Images being generated...
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2011-10-10
Diane Trout
Don't need to duplicate %t tile in srf command
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2011-10-06
Diane Trout
Add the ability to specify a flowcell id instead of...
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2011-10-04
Diane Trout
Add support for flowcells analyzed with Casava 1.7
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2011-09-30
Diane Trout
Sparql query to back create protocol & treatment from...
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2011-09-30
Diane Trout
find submissions, even those without a set creation...
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2011-09-30
Diane Trout
store md5sum of daf files to group different submissions
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2011-09-30
Diane Trout
Configure daf variables in only one place. (daf.py)
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2011-09-30
Diane Trout
Add support for new "extraVariables" term in DAF.
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2011-09-22
Diane Trout
Mark library & flowcell as a type in RDF.
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2011-09-21
Diane Trout
Switch from beautifulsoup to lxml, now that I know...
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2011-09-21
Diane Trout
Rename ucsc submission namespace to be more consistent...
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2011-09-19
Diane Trout
Output samples that don't have index sequence as well.
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2011-09-19
Diane Trout
Python 2.6's DictWriter doesn't have writeheader, so...
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2011-09-17
Diane Trout
Disable csrf protection for the json urls
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2011-09-17
Diane Trout
Add support for tracking the multiplex index sequence.
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2011-09-12
Diane Trout
Add support for first-gen HiSeq flowcells (e.g. ABXX)
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2011-09-08
Diane Trout
Django 1.1's csrf protection appears to be handled...
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2011-09-08
Diane Trout
Add links to the admin page on the public pages if...
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2011-09-08
Diane Trout
Make it so the login link redirects you back to the...
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2011-09-08
Diane Trout
Emacs stripped off trailing whitespace
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2011-09-07
Diane Trout
Add link to admin page to flowcell & library pages...
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2011-09-07
Diane Trout
Remove margin-right command as it was making a giant...
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2011-09-02
Diane Trout
Ignore some files generated by my (diane's) development...
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2011-09-02
Diane Trout
Attempt to download DAF data for a encodesubmit submission
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2011-09-02
Diane Trout
Add error message for requesting link-daf but no daf...
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2011-08-31
Diane Trout
Enable csrf proection when running under Django 1.2
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2011-08-18
Diane Trout
Rescan a flowcell data run once per (setting.RESCAN_DELAY...
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2011-08-08
Diane Trout
Deal with (failed) in flowcell names.
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2011-08-04
Diane Trout
Add a way to browse the list of entered antibody/antigene
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2011-07-29
Diane Trout
Make a test more robust to different versions of librdf
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2011-07-29
Diane Trout
Construct unit tests for inventory/hard disk long term...
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2011-07-28
Diane Trout
Examine the DAF to determine if the DDF needs to include...
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2011-07-20
Diane Trout
Stop copying attributes from library to a submission...
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2011-07-20
Diane Trout
Remove spurious debugging print statement
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2011-07-20
Diane Trout
Add an option to print out an example view to extension...
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2011-07-20
Diane Trout
Make searching library & cell line more robust to missing...
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2011-07-20
Diane Trout
Search for both encode & mouse encode projects.
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2011-07-20
Diane Trout
Update old dt-overrides.turtle example to use the newer...
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2011-07-13
Diane Trout
Make antibody catalog number optional for creating...
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2011-07-13
Diane Trout
Make sure we can roundtrip unicode characters via converting...
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2011-07-09
Diane Trout
Add "Count of multi-reads" back into the library page
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2011-07-07
Diane Trout
Don't use xsd:string for string data types in toTypedNode
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