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2016-04-20Tell redis where to store its persistent dbpjotrp
2016-04-20[PATCH 027/100] Introduce tools.locatePjotr Prins
2016-04-20[PATCH 026/100] Introducing cached values PYLMM_COMMAND,... GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR Pjotr Prins
2016-04-20Introducing TEMPDIRpjotrp
2016-04-20[PATCH 024/100] Sanitizing file handlingPjotr Prins
2016-04-20[PATCH 023/100] WIP fixing all pathsPjotr Prins
2016-04-20Successful startup of GN2 with MySQLpjotrp
2016-04-20Remover dependency to logger_tree (may reintroduce later)pjotrp
2016-04-20[PATCH 018/100] Find external tools: refactored code to work with GNU GuixPjotr Prins
2016-04-20README: add URLpjotrp
2016-04-20* bin/genenetwork2: path handlingpjotrp
2016-04-20Removed import htmlgen as is not used (apparently)pjotrp
2016-04-20* ./bin/genenetwork2: New filepjotrp
2016-04-20Docs: Use ./doc dir instead of ./miscpjotrp
2016-04-20[PATCH 012/100] Adding configuration for running a default serverPjotr Prins
2016-04-20[PATCH 010/100] READMEPjotr Prins
2016-04-20DocsPjotr Prins
2016-04-18Additive effect lines are now separated by chromosome (like the qtl line in t......Fixed order of stats table in trait page Removed the qtl results table from chromosome view; will add the Interval Analyst output later zsloan
2016-04-14Fixed issue where qtl lines in interval mapping wouldn't connect between chro......Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits zsloan
2016-04-13Moved the code getting the description/location because it was throwing an er...zsloan
2016-04-13Global search should be able to return description and location columns nowzsloan
2016-04-11Changed the way trait data is retrieved for the global search page (it now ge......This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line zsloan
2016-04-07Added option to change the maximum y-axis value for GN1 mapping figurezsloan
2016-04-07Permutation figure and x-axis label should change to correctly reflect the ma......Fixed bug where broken image link would appear if you ran R/qtl with no permutations zsloan
2016-04-07SNP Track option should now work for GN1 mapping figure...Fixed typo in show_trait html that caused the p-value slider to not work for correlations zsloan
2016-04-06The option to switch between LRS and LOD for the GN1 mapping figure should no......The correct value (LRS or LOD) will now be displayed in the results table Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc) zsloan
2016-04-06Setting lodm to always be 1.0 fixes the issue where it would incorrectly disp...zsloan
2016-04-06Permutations (suggestive/significant lines, legend, and histogram) should now......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 zsloan
2016-04-05Bootstrap test should now work correctly for qtl reaper mapping method on ful......There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps zsloan
2016-04-05Fixed issue where haplotype analyst option would appear when using genetic(ce...zsloan
2016-03-30Disabled Haplotype Analyst option if mapping scale is centimorgan/geneticzsloan
2016-03-30GN1 mapping now when mapping scale is centimorgan (for R/qtl)...Fixed some issues related to zooming in on chromosome X Fixed problem where it threw an error for mapping methods that didn't return additive effect Fixed problem where the endMb in the top form would be set to the endMb of the last chromosome when viewing full genome zsloan
2016-03-29Additive effect option now works for GN1 mapping figurezsloan
2016-03-29Forgot to add GeneralObject file needed for haplotype analyst in last commitzsloan
2016-03-29Haplotype Analyst now works for GN1 mapping figure...Chromosome drop-down select and Mb range text fields now are set to the values the user last selected zsloan
2016-03-28Legend option now works for GN1 mapping figurezsloan
2016-03-28Trait sample data table width now dynamically changes with number of attribut...zsloan
2016-03-24Graph width can now be set in Mapping Resultszsloan
2016-03-24Add the Gene Track option to display the Gene Band for single chromosome view...Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before) zsloan
2016-03-24Mapping results table is now limited to the top 200 markers; previously the p...zsloan
2016-03-23You can now select chromosome and an Mb range from the top menu and remap...The track in the single chromosome view to zoom into smaller intervals now works correctly again zsloan
2016-03-23Fixed GN1 mapping plots so that Y axis and the Y coordinates of manhattan plo......Table filters markers so it can always be displayed now (previously was too large for GEMMA) zsloan
2016-03-21Manhattan plot option now works for GN1 map, and GEMMA is set to display as m...zsloan
2016-03-21Changed code parsing marker csv file to increase GEMMA speed...Currently commenting out the vector map/table for GEMMA since they cause the page to hang, I'll try to figure out a way to prevent this zsloan
2016-03-18Forgot to not retrieve sample data for the phenotype global search with the l...zsloan
2016-03-18Merge branch 'development' of github.com:genenetwork/genenetwork2zsloan
2016-03-18Replaced header with other information in qtl map...Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary) zsloan
2016-03-17Fixed a bunch of geno files that had most of their contents removed for some ...zsloan
2016-03-15Merge branch 'development' of github.com:genenetwork/genenetwork2zsloan
2016-03-15Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan