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2013-01-31Copied over nginx.conf from /etc/nginxZachary Sloan
2013-01-31Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Deleted nginx.conf from the other_conf directory not in wqflaskZachary Sloan
2013-01-31Merge branch 'flask' of https://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Changed reference to 'dataset_name' in keywords to 'dataset' to getZachary Sloan
page to work, but will change all references to the dataset name to 'dataset_name' in future to avoid confusion between the dataset name and the actual dataset object
2013-01-31Changed fd to kw in search_results.py, commented out some linesZachary Sloan
related to fd
2013-01-25Added a bunch of things to notesZachary Sloan
2013-01-25Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-25Fixed a few bugs while trying to get the code running on the new serverZachary Sloan
2013-01-24Added a lot to the notes in the process of setting up on theZachary Sloan
new server
2013-01-23Added a bunch to notes and created new notes file specificallyZachary Sloan
related to installing a new instance of GN
2013-01-22Added a couple things to notes regarding installing mysql clientZachary Sloan
2013-01-22Pushed through a few errors in getting the correlation page runningZachary Sloan
2013-01-18Renamed CorrelationPage.py to show_corr_results.pyZachary Sloan
Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places
2013-01-11Commented out import of rpy2 in correlationFunction.py due toZachary Sloan
problem with rpy2
2013-01-11Upgraded packages requirements.txt but haven't testedZachary Sloan
2013-01-11Overwrote requirements.txtZachary Sloan
2013-01-11Trimmed a bunch of code off of marker_regression.pyZachary Sloan
2013-01-10Checking in before we try to write our own code for the manhattanZachary Sloan
plot figure`
2013-01-10Checking in before trying to put manhattan plot sections closer togetherZachary Sloan
2013-01-10Normalized the y axis for each manhattan plot sectionZachary Sloan
2013-01-10The plots now correctly appear above/below each other.Zachary Sloan
Committing before trying to combine all the manhattan plot segments
2013-01-10Edited marker_regression.coffee to make every sub-manhattan plotZachary Sloan
for each chromosome display Created css file for the marker_regression page Currently has display issue where the permutation histogram is overlapping with the manhattan plot
2013-01-10Made Chromosome class in marker_regression.coffee; currentZachary Sloan
it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that.
2013-01-10Made x-axis values into ints; committing before trying to add multiple graphsZachary Sloan
for each chromosome
2013-01-10Worked with the manhattan plot coffeescript to set x-axis and changeZachary Sloan
the plot point sizes and remove lines
2013-01-09Manhattan plot results are appearing correctly for chromosome 1Zachary Sloan
2013-01-09The histogram coffeescript is now in its own class and the graphZachary Sloan
still displays correctly
2013-01-09Checking in before putting the histogram coffeescript into its ownZachary Sloan
class
2013-01-09More or less finished the permutation histogramZachary Sloan
2013-01-09Got the permutation plot working as a line plot; still need to makeZachary Sloan
it into a bar graph, though
2013-01-09jqplot addedZachary Sloan
2013-01-09Got the marker regression page to display againZachary Sloan
Passed lrs_array values as js_data for the permutation histogram
2013-01-08js_data is being printed out (seemingly) correctly now for theZachary Sloan
marker_regression page
2013-01-08Created IndChromosome class in species.py and wrote functions forZachary Sloan
chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugsZachary Sloan
Added a couple utility functions to the Chromosomes class in species.py
2013-01-04Continued rewriting marker_regression.py codeZachary Sloan
2013-01-04Correct results are being returned from reaper for the marker regression pageZachary Sloan
2013-01-03Began working on marker_regression.py and created Chromosomes classZachary Sloan
in species.py
2013-01-03marker_regression page is up againZachary Sloan
2013-01-03Created template for marek regression page and made the compute button directZachary Sloan
to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py
2012-12-20Changed layout of marker regression optionsZachary Sloan
2012-12-20The control locus field in the interval mapping settings is now disabled ifZachary Sloan
"choose closest control" is set to "yes"
2012-12-20Made composite mapping options show/hide for the interval mapping sectionZachary Sloan
2012-12-20More changes to the layout of interval mapping optionsZachary Sloan
2012-12-20Continued to customize the interval mapping menuZachary Sloan
2012-12-20Improved appearance/layout of the interval mapping tab using bootstrapZachary Sloan
2012-12-20Form data passed via POST for marker regressionZachary Sloan
Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan
2012-12-18Changed html for the marker regression tabZachary Sloan
Created file show_trait_mapping_tools.coffee to handle submitting the form to the marker regression page Changed form name/id in show_trait.html to "trait_data_form"
2012-12-18Created new file species.py and species class object TheSpeciesZachary Sloan
Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests
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