genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Expand)	Author
2016-06-23	Add warnings for adding MySQLdb cursor	Pjotr Prins
2016-06-18	Changed file permssions to non-executable	Pjotr Prins
2016-05-26	Issue with certain samples (like BXD65a, ones were there are multiple for a s......Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets	zsloan
2016-03-17	Fixed a bunch of geno files that had most of their contents removed for some ...	zsloan
2016-02-08	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development...Conflicts: .gitignore	zsloan
2016-02-08	Removing LFS	pjotrp
2016-02-04	Most importantly, this commit fixes an issue that caused the trait page to no......An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working	zsloan
2015-11-09	Fixed issue that caused mapping to not work; for some reason the path to pylm...	zsloan
2015-07-10	Fixed the genofile_parser.py script since some .geno files had been incorrect......Fixed GO search to work with combined searches	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
2015-05-01	Added Pjotr's latest pylmm changes...Added GEMMA and necessary plink-format genotype files in gemma directory Added the GEMMA genotype files to git LFS Removed some unnecessary/duplicated code from interval_mapping.py Separated GEMMA mapping code into its own file (will also do this for other methods) and fixed and issue that caused it to not run Added the table to the pair scan results page and wrote some code adding its attributes to each marker object, but it still isn't working yet	zsloan
2015-04-10	Added git large file system (the .gitattributes files) and fixed an issue whe...	zsloan
2015-03-27	Removed everything from 'web' directory except genofiles and renamed the dire...	zsloan