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2015-05-12Merge https://github.com/genenetwork/genenetwork2Lei Yan
2015-05-12Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2015-05-12Merge branch 'master' of github.com:genenetwork/genenetwork2pjotrp
2015-05-12Fix #35Artem Tarasov
* 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top
2015-05-11Show PYLMM_PATH on errorPjotr Prins
2015-05-11Moved chunksPjotr Prins
2015-05-11More pylmm dependencies disabledpjotrp
2015-05-11Remove outdated codepjotrp
2015-05-11Moving pylmm out of the treepjotrp
2015-05-11pylmm has moved out of the GN2 source tree to ↵pjotrp
https://github.com/genenetwork/pylmm_gn2
2015-05-08updating histogram on values' change (#28)Artem Tarasov
2015-05-08fix histogram bin widthArtem Tarasov
It was calculated wrongly when bins began from a non-zero value
2015-05-08fixArtem Tarasov
2015-05-08Fix #29Artem Tarasov
The number of bins was set to 20 for all datasets. Changed the number to be sqrt(#samples) as suggested on Wikipedia.
2015-05-07Excel export of trait dataArtem Tarasov
2015-05-07fix CSV export of trait dataArtem Tarasov
2015-05-07allow for attribute table to not existArtem Tarasov
2015-05-06email and pass validationArtem Tarasov
2015-05-01Commented out imports of a few files that aren't used yet or stored in gitzsloan
2015-05-01Added Pjotr's latest pylmm changeszsloan
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
2015-04-10Added git large file system (the .gitattributes files) and fixed an issue ↵zsloan
where rat trait pages wouldn't work
2015-04-06Added secure_server.py to gitignore and fixed conflicts for merging Lei's ↵zsloan
new code
2015-04-06Just committing a couple minor bug fixes to get code working after pulling ↵zsloan
Pjotr's latest changes
2015-04-06Merge branch 'master' of github.com:zsloan/genenetwork2zsloan
2015-04-06Removed the old news code before pulling over Lei's changeszsloan
Removed the SharingPage import from views since it doesn't exist anymore
2015-04-06Merge pull request #3 from pjotrp/masterzsloan
0.50-gn2-pre1
2015-04-06Removed dataSharing directory and its files since they aren't being used,zsloan
but I should note that a couple of them were changed from GN1; I think that there was some attempt to implement this very early into GN2's development, but we'd probably be better off starting from scratch since a number of things have changed since then (such as the way we call queries) Removed the Singapore link from the mirrors section of the index page since it wasn't working
2015-03-31Fixed some aesthetic issues on the main page and removed references to ↵zsloan
TemplatePage
2015-03-30Merge with zsloan masterPjotr Prins
2015-03-27Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ↵zsloan
it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so.
2015-03-27Removed everything from 'web' directory except genofiles and renamed the ↵zsloan
directory to 'genotype_files'
2015-03-26Removed several unused files from the base folder and their references in ↵zsloan
other files
2015-03-25Pair scan image now loads properlyzsloan
2015-03-24Merge branch 'master' of github.com:DannyArends/genenetwork2zsloan
2015-03-24Added pair scan to the marker_regression_page viewzsloan
2015-03-24Added back css directory/fileszsloan
2015-03-24Change back port location and home directory location; this should be in ↵zsloan
external settings
2015-03-24Updates to the templateszsloan
2015-03-24Code updates to marker regressionzsloan
2015-03-24Removing the node.js + v8 code from the repository (this should be also ↵DannyArends
removed in the history), this should not be here since its a dependency not code we want to maintain ourselves
2015-03-23Minor update to get the pylmm code working on my instance of penguinDannyArends
2015-03-23Updates to make GN2 work on my version of penguin (ports, and paths)DannyArends
2015-03-23Adding my path to sys.path in pylmmDannyArends
2015-03-23Merge branch 'master' of github.com:pjotrp/genenetwork2DannyArends
2015-03-20Merge branch 'master' of https://github.com/zsloan/genenetwork2Pjotr Prins
2015-03-19Removing mapmethod mapmodel from the coffeescriptDannyArends
2015-03-19testing some moreDannyArends
2015-03-19Print initial start_varsDannyArends
2015-03-19Print wantedDannyArends
2015-03-19Print for testingDannyArends