genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Expand)	Author
2015-12-14	GN1 mapping full genome figure now correct for pylmm and output to web page	zsloan
2015-12-12	Changed loop drawing qtl curve to fix some issues; still need to make it draw...	zsloan
2015-07-09	Mapping methods now check for existing genotype files....Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory	zsloan
2015-03-27	Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ...	zsloan
2015-03-25	Pair scan image now loads properly	zsloan
2015-03-24	Change back port location and home directory location; this should be in exte...	zsloan
2015-03-23	Updates to make GN2 work on my version of penguin (ports, and paths)	DannyArends
2013-08-07	Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user password, etc	Zachary Sloan
2013-07-19	Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist	Zachary Sloan
2013-07-18	Added Amelie's rat data genotypes...Got human mapping mostly working Fixed dataset dropdown menus	Zachary Sloan
2013-07-18	Added to installation notes...Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json)	Zachary Sloan
2013-06-13	Merge /home/sam/gene into flask...Conflicts: wqflask/wqflask/templates/index_page.html Merging the code on Sam's branch onto my own	Zachary Sloan
2013-04-17	Created file with pickled SNPIterator (from input.py) data...for HLC datasets Still need to read in file	Zachary Sloan
2013-04-02	pylmm code is running for human data (plink .bed genotype files)	Zachary Sloan
2013-02-07	Added code to marker_regression.py that creates the numpy arrays to...pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited	Zachary Sloan
2013-01-25	Fixed a few bugs while trying to get the code running on the new server	Zachary Sloan
2012-05-24	Trying to get stuff working under new structure	Sam Ockman