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2016-10-12Moved plink code out of marker_regression, though I don't think plink is ↵zsloan
working right now Ran some end of line conversion on rqtl_mapping because there were a few ^M's
2016-10-12Removed unused gemma code from marker_regression.py and changed the order of ↵zsloan
a couple functions in collect.py to more accurately reflect when they're called
2016-10-07Removed qtlreaper code from marker_regression and moved it to a separate file.zsloan
Fixed CTL template to display correct number of traits (previously it would display 1 fewer than you selected).
2016-10-07Saner handling of TMPDIR and TEMPDIRPjotr Prins
Throw error when TMPDIRs are not writable
2016-10-06URLs: replaced non-functioning URLsPjotr Prins
2016-10-06Footer: updating URLsPjotr Prins
2016-10-06Do not open new page in browser on URLPjotr Prins
2016-10-06Removed dead URLPjotr Prins
2016-10-06URL: replaced dead Memphis URL with current GN2 machinePjotr Prins
2016-10-06URL: prevent opening new pagesPjotr Prins
2016-10-06URL: updated Amigo reference on front pagePjotr Prins
2016-10-06URLs: update GO database URL and removed opening new browser pagesPjotr Prins
2016-10-06Logger: add more granular debug messagesPjotr Prins
2016-10-06CTL requires 2 traits minimally. Also use traits/phenotypes consistentlyPjotr Prins
2016-10-05CTL now displays proper error if fewer than 4 traits are selected. Also, ↵zsloan
WGCNA previously incorrectly gave an error when fewer than 5 traits were selected instead of fewer than 4 (because it said '<= 4'). I also improved the formatting for the html for both CTl and WGCNA Analysis.
2016-10-05Show datasets only on debugPjotr Prins
2016-10-05Minor editPjotr Prins
2016-10-05Reverted on genotype selector on page show_trait_mapping_tools.html - ↵Pjotr Prins
pending the full PR
2016-10-05print statements should be loggerPjotr Prins
2016-10-05print statements should be loggerPjotr Prins
2016-10-05Merge branch 'zsloan' into jsonPjotr Prins
2016-10-05Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2016-10-04Fixed issue that caused adding to existing collections when not logged in to ↵zsloan
not work correctly. The problem was that it would get the collection name from the "new_collection" field instead of the "existing_collections" dropdown.
2016-10-04Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2016-10-03Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2016-10-03Fixed problem that caused R/qtl with permutations to not work correctlyzsloan
2016-10-03Moved rqtl mapping code out of marker_regression and into its own file.zsloan
Later we will want to run all mapping methods outside of the web server, though
2016-10-03Config: supporting JSON OVERRIDESPjotr Prins
2016-10-03Debug: sanitize some outputPjotr Prins
2016-10-03Config: use server port settingPjotr Prins
2016-10-03Error page: reduce cookie sizePjotr Prins
2016-10-02Error page: trim error messagesPjotr Prins
2016-10-02Errors: added time stamps in UTCPjotr Prins
2016-10-02Error page: also display the URLPjotr Prins
2016-10-02Merge branch 'master' of github.com:genenetwork/genenetwork2Pjotr Prins
2016-10-02Error page: use cookies to fixate the animation for one errorPjotr Prins
2016-10-02Error: remove test errorPjotr Prins
2016-10-02Error screen improvements with animated gifsPjotr Prins
2016-09-30Merge pull request #192 from lyan6/masterPjotr Prins
Fix global search "il6" for "Internal Server Error". Add single quote…
2016-09-30Add missing __init__.pyPjotr Prins
2016-09-30Add logging for qtlreaperPjotr Prins
2016-09-29Fix global search "il6" for "Internal Server Error". Add single quotes into ↵Lei Yan
MySQL query.
2016-09-27Conflict in wqflask/wqflask/templates/show_trait_mapping_tools.htmlzsloan
2016-09-26Test: mechanical Rob executes scanone testPjotr Prins
2016-09-25Logger: use output for assessing mapping parametersPjotr Prins
2016-09-25Make sure MAPPING_PATH existsPjotr Prins
2016-09-25Settings: enforce MAPPING_PATH only when running plink_gemmaPjotr Prins
2016-09-25I was getting below error with the small database. This commit, at least, doesPjotr Prins
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'
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-09-13Save Image now works for Network Graph and downloads current graph as a pngzsloan
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