chipathlon merge requestshttps://git.unl.edu/hcc/chipathlon/-/merge_requests2017-01-30T14:37:13-06:00https://git.unl.edu/hcc/chipathlon/-/merge_requests/11Resolve "Module generator improvements"2017-01-30T14:37:13-06:00aknecht2Resolve "Module generator improvements"Closes #8
Lots of important adjustments in module_generator & individual modules. Module generator has been refactored to use new result/run/genome classes.Closes #8
Lots of important adjustments in module_generator & individual modules. Module generator has been refactored to use new result/run/genome classes.Workflow Module RefactorNatasha PavlovikjNatasha Pavlovikjhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/10Minor fixes to the genome class2017-01-26T15:04:50-06:00aknecht2Minor fixes to the genome classMissed some stuff before merging. Oops.Missed some stuff before merging. Oops.Workflow Module RefactorNatasha PavlovikjNatasha Pavlovikjhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/9Resolve "Create genome class"2017-01-26T14:49:24-06:00aknecht2Resolve "Create genome class"Closes #9Closes #9Workflow Module RefactorNatasha PavlovikjNatasha Pavlovikjhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/8Resolve "Adjust input run.yaml format"2017-01-26T09:43:30-06:00aknecht2Resolve "Adjust input run.yaml format"Closes #2 Updates the run_parser to create new run class / genome class objects. #9 still not resolved, dummy class was used for testing.Closes #2 Updates the run_parser to create new run class / genome class objects. #9 still not resolved, dummy class was used for testing.Workflow Module Refactorhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/7Resolve "Create result class"2017-01-25T19:06:01-06:00aknecht2Resolve "Create result class"Closes #6
Adds a result class to handle intermediate output instead of managing everything in a giant dictionary structure. Instances of result class will be added to the new Run class to manage data better.Closes #6
Adds a result class to handle intermediate output instead of managing everything in a giant dictionary structure. Instances of result class will be added to the new Run class to manage data better.Workflow Module RefactorNatasha PavlovikjNatasha Pavlovikjhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/6Resolve "Create new run data class"2017-01-22T21:48:16-06:00aknecht2Resolve "Create new run data class"Created new Run class. Added tester methods to validate samples loaded by run.
Closes #10Created new Run class. Added tester methods to validate samples loaded by run.
Closes #10Workflow Module RefactorNatasha PavlovikjNatasha Pavlovikjhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/36Modify chip-meta-import to first try and set the genome type based on the sample2017-08-03T11:06:25-05:00Natasha PavlovikjModify chip-meta-import to first try and set the genome type based on the sampleModify chip-meta-import to first try and set the genome type based on the sample file information instead of the experimentModify chip-meta-import to first try and set the genome type based on the sample file information instead of the experimentAdam CaprezAdam Caprezhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/35Add resume option to meta download script.2017-07-06T16:46:34-05:00Adam CaprezAdd resume option to meta download script.Fixes #36.
Closes #36Fixes #36.
Closes #36Adam CaprezAdam Caprezhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/34Resolve "Zerone"2017-06-14T13:11:18-05:00aknecht2Resolve "Zerone"Closes #26
Woo!Closes #26
Woo!aknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/33Resolve "MongoDB auth should be optional"2017-06-08T14:33:53-05:00aknecht2Resolve "MongoDB auth should be optional"Closes #34Closes #34aknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/32Bridges compatability2017-06-08T11:12:38-05:00aknecht2Bridges compatabilityUpdates so things work on bridges as well as on local submit sites.Updates so things work on bridges as well as on local submit sites.aknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/31Exclude *.pyc files when loading executables.2017-05-12T11:02:39-05:00Adam CaprezExclude *.pyc files when loading executables.Closes #33Closes #33Adam CaprezAdam Caprezhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/30Resolve "Setuptools fixes"2017-05-11T16:43:15-05:00Adam CaprezResolve "Setuptools fixes"Closes #32Closes #32Adam CaprezAdam Caprezhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/29Resolve "Remove module load from wrappers"2017-05-11T16:23:49-05:00Adam CaprezResolve "Remove module load from wrappers"Closes #31Closes #31Adam CaprezAdam Caprezhttps://git.unl.edu/hcc/chipathlon/-/merge_requests/28Resolve "Update Default Params"2017-05-08T10:16:46-05:00aknecht2Resolve "Update Default Params"Closes #30Closes #30aknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/27Resolve "MUSIC peak caller"2017-05-04T12:17:54-05:00aknecht2Resolve "MUSIC peak caller"Closes #24Closes #24Peak Calling / Idraknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/26Resolve "Documentation In-Depth"2017-04-25T15:24:31-05:00aknecht2Resolve "Documentation In-Depth"Closes #28Closes #28https://git.unl.edu/hcc/chipathlon/-/merge_requests/25Resolve "Method Auto Doc"2017-04-13T15:21:29-05:00aknecht2Resolve "Method Auto Doc"Closes #3Closes #3Documentationaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/24Sphinx Building2017-04-12T13:50:09-05:00aknecht2Sphinx BuildingInitial sphinx doc stuff created!
Closes #27Initial sphinx doc stuff created!
Closes #27Documentationaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/merge_requests/23Script updates2017-04-05T10:53:25-05:00aknecht2Script updatesCloses #14Closes #14Input Parsingaknecht2aknecht2