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2016-09-25Merge branch 'master' into chfiPjotr Prins
2016-09-25Testing: looking for a way to run pylmmPjotr Prins
2016-09-25I was getting below error with the small database. This commit, at least, does...not assume the item exists. ERROR:wqflask:Exception on /marker_regression [POST] Traceback (most recent call last): File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1817, in wsgi_app response = self.full_dispatch_request() File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1477, in full_dispatch_request rv = self.handle_user_exception(e) File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1381, in handle_user_exception reraise(exc_type, exc_value, tb) File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1475, in full_dispatch_request rv = self.dispatch_request() File "/home/wrk/.guix-profile/lib/python2.7/site-packages/Flask-0.10.1-py2.7.egg/flask/app.py", line 1461, in dispatch_request return self.view_functions[rule.endpoint](**req.view_args) File "/export2/izip/git/opensource/genenetwork/sumo_gn2/wqflask/wqflask/views.py", line 460, in marker_regression_page template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) File "/export2/izip/git/opensource/genenetwork/sumo_gn2/wqflask/wqflask/marker_regression/marker_regression.py", line 74, in __init__ value = start_vars['value:' + sample] KeyError: 'value:BXD80' Pjotr Prins
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-25Doc: Section on reproducibility... - fixed SVG URLs Pjotr Prins
2016-09-16Refetch SNP density on zoomchristian
2016-09-13Save Image now works for Network Graph and downloads current graph as a pngzsloan
2016-09-13Fixed the path for the json file in gen_select_dataset.py since it was wrong ......Added "Reset" option to network graph that returns all the nodes/edges Made the visualization options area in the network graph a little wider zsloan
2016-09-13Merge pull request #181 from pjotrp/zsloan...Run scripts from ./wqflask - just like the webserverzsloan
2016-09-13Run scripts from ./wqflask - just like the webserverPjotr Prins
2016-09-12Merge pull request #180 from pjotrp/zsloan...Support maintenance scriptszsloan
2016-09-10CommentPjotr Prins
2016-09-10Support for running maintenance scripts so they can pick up all webserver set......Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py Pjotr Prins
2016-09-10Merge branch 'development' of github.com:genenetwork/genenetwork2 into zsloanPjotr Prins
2016-09-10Doc: Rpy2 notePjotr Prins
2016-09-09Added a couple options for network graph - Focus Trait, Layout, and a correla......Changed/added a couple node/edge attributes for network graph Updated dataset menu structure json file to include the human RETINA data set Added css file for network graph page (specifically to make the appearance of the options resemble the RETINA website's) zsloan
2016-09-09Merge branch 'master' of github.com:genenetwork/genenetwork2Pjotr Prins
2016-09-09Doc: note on guix pathsPjotr Prins
2016-09-08Fix genotype & QTL plot vertical scalingchristian
2016-09-02Added Network Graph feature that uses cytoscape.js. Currently you can view GN......Fixed issue that caused error with correlation page zsloan
2016-08-26Fixed appearance (border width mostly) of basic stats table on trait page...Removed unnecessary datatables javascript code that referred to basic stats table zsloan
2016-08-24Fixed issue causing bootstrap results to not plot correctly.zsloan
2016-08-24Replaced post-publication description with pre-publication description for co......Fixed table style for mapping results and interval analyst tables and added additive/dominance effect columns to the former Fixed mapping figure X-axis to accurately label Centimorgans vs Megabases (previously it would always say Megabases) Removed the "Sequence Site" marker from mapping result figure when mapping with genetics (centimorgans) scale Removed some unused javascript libary imports from search/global search pages zsloan
2016-08-19Merge branch 'biodalliance' of github.com:chfi/genenetwork2 into chfiPjotr Prins
2016-08-17Updated dataTables from 1.10.8 to 1.10.12 on search result pagezsloan
2016-08-17Fixed problem where Year column didn't sort properly in phenotype search and ...zsloan
2016-08-17Hide "close BD" button when returning to full viewchristian
2016-08-17Merge branch 'staging' into chfiPjotr Prins
2016-08-17Merge branch 'gn_server' into chfiPjotr Prins
2016-08-17Use this.urlPjotr Prins
2016-08-17Fix SNP stylesheet to fit new bin sizechristian
2016-08-16Users can now select specific traits from collection when using collection to......To do the above, changed the way form submission worked for those features; previously each feature had its own form, but that was dumb so instead I wrote a javascript function that just changed a single form's target url Duplicate traits can no longer by added to collections Fixed the digits for a few table columns in collection (additive effect, etc). zsloan
2016-08-16Add SNP density track to BD browserchristian
2016-08-15Removed text recommending winsoring when mapping since that feature isn't imp......Added padding to header text of Basic Statistics table zsloan
2016-08-15Fix genotype source, interval mapping issuechristian
2016-08-14Check routing paths: notice use of this.urlPjotr Prins
2016-08-14Default settingsPjotr Prins
2016-08-12Changed pop-up asking to import collections to less obtrusive checkbox...Decreased collections/list table width zsloan
2016-08-12Add genotype trackchristian
2016-08-12Increase height of BDchristian
2016-08-11Added prompt when user logs in that lets them choose to import existing anony...zsloan
2016-08-10Rewrite BD sources; use computed QTL data in BDchristian
2016-08-10Serve QTL data as CSVchristian
2016-08-09Use JSON served as file for marker_regression datachristian
2016-08-09Serve marker_regressions data as JSON filechristian
2016-08-09Use correct webworker prefix for BDchristian
2016-08-08Fixed bug where Interval Analyst result wouldn't appear for chromosome X in m......Fixed broken image link in Interval Analyst table for rats Small change to column width of gene global search zsloan
2016-08-08JS: check whether download paths existPjotr Prins
2016-08-08Merge branch 'biodalliance' of github.com:chfi/genenetwork2 into gn_serverPjotr Prins
2016-08-08BD: reverted on build in path so CSS is seen againPjotr Prins
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