genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-06-21	Benchmarking: allow output select with LOG_BENCH	Pjotr Prins

2016-06-21	Logger: SQL	Pjotr Prins

2016-06-19	gn_server: Species info can be fetched from gn_server	Pjotr Prins

2016-06-19	gn_server: SQL handling	Pjotr Prins

2016-06-19	Logger: started logging SQL	Pjotr Prins

2016-06-19	logger: adding functionality for SQL	Pjotr Prins
	views.py: simplified code
2016-06-19	Renamed settings so they are grouped together	Pjotr Prins

2016-06-18	Logger: changed level	Pjotr Prins

2016-06-18	Logger: create stub so we can have multiple arguments to log functions	Pjotr Prins

2016-06-18	Logging settings	Pjotr Prins

2016-06-18	Documented logger	Pjotr Prins

2016-06-18	Logger: more info	Pjotr Prins

2016-06-18	Logger: introducing logging	Pjotr Prins

2016-06-18	Logging: behaviours	Pjotr Prins

2016-06-18	Logger: improving output	Pjotr Prins

2016-06-18	Changed file permssions to non-executable	Pjotr Prins

2016-06-18	Disable setting sys.paths	Pjotr Prins

2016-06-18	Logger: introducing logging	Pjotr Prins

2016-06-17	Conflict	Pjotr Prins

2016-06-17	Removed trailing spaces in .py and .js files	Pjotr Prins

2016-06-16	Introduce behaviour parameters to facilitate development	Pjotr Prins

2016-05-17	Merge branch 'staging' of github.com:genenetwork/genenetwork2	zsloan

2016-05-10	Correlation successfully uses materialized views and parallel processing, ↵	zsloan
	but for some reason is taking an immense amount of time so need to troubleshoot that Changed order of mapping options to display Interval Mapping first Changed some links to no longer open in new tab/window
2016-04-20	A few fixes to get the webserver running again	Pjotr Prins

2016-04-20	Parsing the names of the individuals, and coding H as -999	DannyArends

2016-04-20	Adding the geno file parser from Zach	DannyArends

2016-04-20	Show error when GENODIR is missing	Pjotr Prins

2016-04-20	external program should fail on return value not zero	pjotrp

2016-04-20	Minor fixes	pjotrp

2016-04-20	[PATCH 042/100] Sanitizing locations	Pjotr Prins

2016-04-20	[PATCH 041/100] Fixes for running tools	Pjotr Prins

2016-04-20	-a	Pjotr Prins
	[PATCH 038/100] Fix compile errors
2016-04-20	[PATCH 037/100] WebQtlConfig: sanitizing naming and used vars	Pjotr Prins

2016-04-20	Settled on the _COMMAND syntax over _RUN	pjotrp

2016-04-20	[PATCH 033/100] Refactored file searching	Pjotr Prins

2016-04-20	Fine tuning file locating	pjotrp

2016-04-20	tools.py: add function locate_without_error	pjotrp

2016-04-20	[PATCH 027/100] Introduce tools.locate	Pjotr Prins

2016-04-20	[PATCH 026/100] Introducing cached values PYLMM_COMMAND,	Pjotr Prins
	GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
2016-04-20	Introducing TEMPDIR	pjotrp

2016-04-20	[PATCH 024/100] Sanitizing file handling	Pjotr Prins

2016-04-20	[PATCH 023/100] WIP fixing all paths	Pjotr Prins

2016-04-20	[PATCH 018/100] Find external tools: refactored code to work with GNU Guix	Pjotr Prins

2016-04-07	SNP Track option should now work for GN1 mapping figure	zsloan
	Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06	Permutations (suggestive/significant lines, legend, and histogram) should ↵	zsloan
	now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
2015-11-09	Fixed issue that caused mapping to not work; for some reason the path to ↵	zsloan
	pylmm was wrong
2015-07-09	Mapping 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
2015-06-29	Merge pull request #72 from lomereiter/issue69	zsloan
	Fixes #69
2015-06-29	Merge pull request #77 from lomereiter/fix_sql	zsloan
	SQL security fixes
2015-06-26	Fixed bug where mapping results sometimes wouldn't display. This would occur	zsloan
	due to a chromosome (in this case the last) not having any markers. Improved the way plink gets its path/command to use a method similar to the one Pjotr used with pylmm. I'll also do this for the other mapping methods. Fixed issue where the Y axis would always say LOD score. It now says LRS for mapping methods that return LRS Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary) Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results in a new page. I had resolved every issue but the mapping javascript (lod_chart) not being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty sure that this is because js_data was inserted into the html after the page was loaded while the chart code ran immediately. I experimented with adding a short timeout to the mapping javascript and data table javascript, but while it worked for the table it did not work for the mapping figure. I don't know why this is.