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2018-05-25Fixed issue causing anonymous collections to not work on my branch and ↵zsloan
staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
2018-05-17Added script to quantile normalize a data set and enter its normalized ↵zsloan
sample data into ElasticSearch Added option to replace trait page sample/strain values with normalized ones Began editing Lei's scatterplot code Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
2018-04-23Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter ↵zsloan
instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
2018-04-16Resolved conflicts after pulling changeszsloan
2018-04-12README and docsPjotr Prins
2018-04-09Removed unused code from get_select_dataset.py and get_group_samplelists.py ↵zsloan
scripts
2018-04-09Removed unused code from convert_geno_to_bimbam.py and corestats.pyzsloan
2017-12-06Fixed drop-down group orderzsloan
2017-12-04Fixed drop-down scripts to more appropriately deal with BXD300 groups ↵zsloan
(though there's still a minor issue with a few datasets) Added some header data to mapping output file Fixed links in Network Group nodes/edges
2017-11-06Replaced Histogram and Bar Chart with Plotly version and added new Box Plot ↵zsloan
with Plotly GEMMA now has option to select genotypes Updated dataset select dropdowns to be ordered correctly Fixed dataset select dropdowns for correlations to not show confidential datasets Added Skewness and Kurtosis to Basic Statistics table Fixed Verify and RNA-seq buttons on trait page Temporarily hardcoded Reference page until we get it to link with database
2017-09-07Added the script to convert bimbam to kinship matriceszsloan
2017-09-05Added file converting genofiles to bimbamzsloan
2017-05-21Merge from the diet branch.Pjotr Prins
* refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile
2017-02-08Changed the way .fam files are written/read, which fixes the issue with ↵zsloan
GEMMA mapping accuracy.
2016-12-12Moved a bunch of functions out of the GeneralTrait class that didn't need to ↵zsloan
be there and changed the code that calls them accordingly Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json
2016-09-30Add missing __init__.pyPjotr Prins
2016-09-13Fixed the path for the json file in gen_select_dataset.py since it was wrong ↵zsloan
and uncommented simplejson import Added "Reset" option to network graph that returns all the nodes/edges Made the visualization options area in the network graph a little wider
2016-09-13Run scripts from ./wqflask - just like the webserverPjotr Prins
2016-09-10CommentPjotr Prins
2016-09-10Support for running maintenance scripts so they can pick up all webserver ↵Pjotr Prins
settings Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
2016-07-16README: added infoPjotr Prins
2016-06-19Renamed settings so they are grouped togetherPjotr Prins
2016-06-18Changed file permssions to non-executablePjotr Prins
2016-06-18Disable setting sys.pathsPjotr Prins
2016-06-17ConflictPjotr Prins
2016-06-17Removed trailing spaces in .py and .js filesPjotr Prins
2016-06-16Generating the menu is now obsoletePjotr Prins
2016-04-20More hard-codedpjotrp
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-02-18Edited gen_select_dataset to remove confidential datasetszsloan
Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
2016-01-29Info button should now work for phenotype and genotype datasetszsloan
2016-01-27Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-01-27Added info button to Dataset dropdown on index pagezsloan
Fixed script that generates dataset dropdown json file to include accession id Fixed dataset link on search results page
2016-01-26Removed a bunch of files/directories/packages that are no longer used and ↵zsloan
some corresponding imports
2015-07-09Forgot to add one change to the last commitzsloan
2015-07-09Mapping methods now check for existing genotype files.zsloan
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
2015-05-11Fixed gen_select_dataset so that it does not include Phenotype andzsloan
Genotype groups when the corresponding data sets do not exist Interval Mapping no longer shows up for human traits Fixed the appearance of the mirror links on the main page
2014-08-28Added a validation that warns the user of the number of permutations forZachary Sloan
pyLMM is more than 20 (due to speed) Changed the port in the flask settings to 5002 due to adding the new production server branch
2014-07-14Merge /home/zas1024/geneLei Yan
Conflicts: wqflask/wqflask/static/new/javascript/dataset_select_menu.js wqflask/wqflask/templates/corr_scatter_plot_old.html
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2014-03-05Improved load_genotypes.pyLei Yan
Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master
2014-02-28Made some changes to Lei's IO code for GN1 and GN2 genofilesLei Yan
2014-02-23On branch masterLei Yan
2014-02-23On branch masterLei Yan
2014-02-23On branch masterLei Yan
2014-02-22On branch masterLei Yan
2014-02-22On branch masterLei Yan
2014-02-22On branch masterLei Yan
2014-02-22On branch masterLei Yan
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